I'm going to ask some questions regarding the printed campaign books of the Rogue Trader line, consisting of Lure of the Expanse, Edge of the Abyss, and the Warpstorm Trilogy. Seeing as these are fun things to do, I will endeavor to limit spoilers, if you can't keep yourself from reading on (as opposed to the tl;dr I'm sort of more expecting ), but this is the warning, ahead of time...

THERE WILL BE SPOILERS!!!!

1. Lure of the Expanse: So, some of the worlds, I get it; there are things about them that make it difficult to leave, once you find the place, or something; you might even be the first people to actually go there, among Humanity, but two, in particular, Vaporius, and Zayth, have some interesting-ish optional Endeavors, if you are feeling like you can afford to drag your feet, on the way to the Dread Pearl, or you go back, after Lure is concluded. That's nice, but WHY are these still available Endeavors? Certainly, a few people have been to these worlds. Members of the Adeptus Mechanicus have already visited Zayth, and low-ranking Priests already got somebody to take them to Vaporius, and tried to convert the people away from the Priest-Kings, and into the bosom of the God-Emperor. How is it, then, that no one else has already taken the opportunity to exploit the optional money from the water, or the tech? You're not the first Rogue Traders to visit, even excluding your rivals (who are kind enough to give you just an idea of how many different Rogue Traders, and their dynasties, are active, JUST in the Expanse, roughly one sector of space?), or you wouldn't have any real info on the planets, in question, so, if you might be avaricious enough, while on a strict time table, why wouldn't someone else, who was just passing through?
2. The Warpstorm Trilogy: throughout the adventures of this three-part funfest, you encounter four additional Rogue Traders. Two of them, Scourge and Feckward, you can look up in Lure, and see their listed Profit Factors, but the other newbies, Orleans and Amardi, are brand new, and the books don't hint at their PF, if you might need it. Is there a good average? Both seem reasonably successful, so I'd say somewhere in the 40-55 range, but I'm not sure if they basically planned to say "they seem about as good as you are, success-wise, so whatever your group has, theirs is +/- 5 PF", or if the shape of the campaign, and the Social Endeavors, coupled with the important people who DON'T have PF, like Locke, made them skip it, but I'm unsure how to guesstimate what your "typical" Rogue Trader should have.
3. Frozen Reaches: why can't they ever use their own stinking math right? They give you rules for how to calculate values, and then you check theirs, and they don't work out. You want to add your ship to Damaris' defense? It's type has a value, and then its Crew Quality adds to that, simple enough. My cruiser with a Crack (40) CR should be 24. This works, till the glass cruiser Ordained Destiny comes in 10+ points shy, while the light cruiser Aegis comes in +10 points over. I know the one is weaker than normal, and he doesn't want to risk losing it, as much, but are they using Locke's Void Tactician? Orleans doesn't seem to be? Can you? I get that they often build NPCs just bit by bit, taking nothing into account of how you have to build your PCs, but they should try to make it make sense, before I try to use it, comparing to the written examples, just to find out that they aren't "typical". Ground units, and air support assisting them, don't seem to hold much better, based on their rules. This might just be, in part, the not-so-popular Mass Combat rules...
4. Citadel of Skulls: This one feels rather simple, most of the way through, right up to the end, and it brings two questions: how much of the Vault can you really tear out of the ground, and carry back up to your ship, and with what, while your ship is being blasted by Chaos, and your better than Crew scores are with you, and not it? Second, if you can really take most of the Vault, as the book implies, and you read over the list of things in it, how do you justify the players walking away with so MUCH weird, awesome loot? Even excluding the Rhino-sized thing you are actually supposed to take, it's full of some nix-level stuff, and in large quantities.
5. Elite Advances: how liberal are you with some of these? As I said, the NPCs are built more haphazardly, without any real path they follow, like you do, so they might often have things you can't, like the aforementioned Void Tactician (only Void Masters can get it at all early, and none of these examples are that; they are Captains, or leaders of some other stripe), even though their overall build seems lower in cost than yours. They might do this to make them more challenging, in specific fields, since they often feel like they were built for maybe lower levels, but it can be hard to tell. How lenient are you going to be if the PCs ask for similar treatment, if they have the XP, and are willing to spend the extra you require?
6. Self vs. Squad: okay, so some of your abilities, talents, and such are "group affecting", if you will. If you are there, and have Enemy, and your group is dealing with the enemy, they all probably get the penalty, too, as you are known to them. In this way, every PC contributes to the face of their Rogue Trader's dynasty, rather than just the scion, being escorted by minions. I like this, but how do other things work for this. I'm going to use Void Tactician, again, sorry. Your GM is a bit strict on EAs, so only the Void Master is likely able to get it, prior to the end of this campaign. In said space battle, she is piloting the ship, however, while the Arms Master is directing the gun crews, with his superior BS characteristic. With the whole crew aboard ship, does the ship's actions in combat still get this talent, or is it only if the VM stops piloting, and starts shooting? If so, why do some of the NPC leaders have it, if they aren't the ones pulling the trigger? Can she pull off both, even as most of either is done remotely, or must she focus on one, and leave the other to another player/the crew?
7. Rarer Gear: where do you get some of these? I imagine some places actually do have "weapons shops", where you could buy guns, maybe even light armor, and your standing in Imperial society, coupled with a veritable world's worth of resources, could let you deal with some military entities/armories, but there are some toys the Imperium just doesn't seem to produce in bulk, like Field-generating items, yet many Rogue Trader-types have them. When your party is setting out on their adventures, and have an idea of what types of flashy gear they want to use, where can they acquire some of these things? There shouldn't be that many Forge Worlds, and they probably won't want money, etc. On the other hand, cool as a Refractor Field is, it seems ridiculous to go on a whole Endeavor, at the behest of the AdMech, just so one character can get one piece of not-legendary equipment, be it the field, maybe a BQ plasma pistol, or something similarly rare. Do some of the PDF armories just have them, in reserve, and sell them? With some of these worlds being so long separated from the Imperium, I'm not even often sure where they get some of their toys, but that can be for later.

Okay, I've babbled enough. If you've gotten to this point, and NOT just tl;dr-ed, thank you very much, and if you are this far, and feel more than just irritated at the pointlessness of the questions, I'd love to hear some answers/opinions. Hopefully, somewhere in the incessant whining, you found the actual queries I was positing, and have something to add. Thanks much, and please have a good one.

All of these are my explanations, and not to be taken as granted

1) For Vaporious, the water is super addictive, and the Priests (if not the Priest Kings) know it. Eventually customers who get hooked on this die horribly, or would tear a Rogue Trader to pieces to try and secure their own supply. It might give you a short boost in profit factor, but it'll all end horribly. As for the Ministorum, Vaporious has recognised the power of the Imperium and slowly drags their feet on conversions to draw it out. Getting people hooked on their water is helpful in securing few questions.

2) You can always take the book's approach and guess at their SP value, then subtract that from the starting value of 90 (I think, don't have my book). Your guesses seem reasonable

3) There is no good answer for this. Run a small space battle with your players and extrapolate that for dramatic purposes is how I handled this.

4) Haven't run this one, so can't comment. Certainly your concerns seem valuable, so force your players to make several trips. Every trip roll a cumulative 10% chance of the Chaos bombardment causing horrible catastrophe? Season to taste for yourself. Ultimately looting a Chaos horde should cause its own problems.

5) I am reasonably liberal with them if they make sense. I charge usually 300 per skill, 750 per talent, but will lower it as needed. If it's something the players have tried and failed at (and accepted failure) then I'll let it happen. My Astropath spent three sessions crashing Dark Eldar Jetbikes around until he passed a 1/4th Agility test twice in a row, and then it was a normal advance. Once his arm healed.

6) I limit PCs to what it is they are actually doing, and then NPCs I'm more liberal with because they get murdered in combat anywhere.

7) Weapon sales are extremely high in places like the Expanse, but it does get a little more tricky in Imperial space. However outside of it where technology is far, far less strictly controlled and most of your clientele ARE Rogue Traders, then I think it makes a lot more sense people would be willing to sell these. Note this is the advantage of the Acquisition system, because it represents money changing hands, and then they "know a guy" who will get the item delivered - eventually. None of these are through entirely legal channels, but by default they're just shady, not illegal.

1: Who's to say there isn't already people dealing with and exploiting these places? Zayeth for sure. The PC's might decide to make a deal with what, one of the ships? I mean there's dozens of land ships, and if I recall some sort of space station for ships to dock and repair above the world. Sounds like the sort of place that does some trade now and again.

Vaporius is a little more meh. I could see it going poorly for people that try to make a long term go of it Run afoul of the inquisition, get screwed over by the kings of Vaporius, or just any of the other of many potential problems dealing with trade in the Expanse.

2: Dunno. Don't remember that one off the top of my head.

Page 270 of the core book does give you a list of what the various profit factors mean, so nothing's stopping you from assigning one that looks appropriate.

40 Lesser rogue trader.

70 Wealthy rogue trader.

3: The math is for the PC's, for the NPC's they've assigned an arbitrary number that looks right. Loke's a better captain in a war campaign, more dedicated to the cause, and so on, so I can see her ship being worth more, while Blitz is worth less for being an opportunist and more of a rogue adventurer than a seasoned naval captain. Seems reasonable to me.

4: That's for the players to figure out and get creative. The only thing you “have” to get is something that your average lighter can haul, and they even give you a method to get it to the surface. Want to take more? Call down a few more lighters or even a halo barge, just be ready to protect your booty while you wait for the second ride to arrive.

5: I go with “Costs double what it costs for people that get it at that level.” If you want early access, either for your own career or for something other careers get later on, then it's going to cost more. If you set up the ground work and training I'll reduce the extra cost by half (resulting in a 150 or 200% cost depending).

6: It's going to depend on the wording of the talent in question. Void tactician is a little vague on the wording, but it seems to say that it is granting the bonus to the one with the talent. So if your voidmaster is the one shooting the guns (use his ballistics skill and any actions required) then he gets the bonus. If it's someone else shooting the guns and he's concentrating on something else, then no. But it's a case by case thing depending on the talent or ability.

7: The acquisition/profit factor system is left vague on purpose. It's up to the GM and Players to decide what combination of money, influence, contacts, and negotiation result in an acquisition. Take a look at the particular item and the market the purchase is being made in, and you'll probably be able to figure out a reasonable source for it.

In the case of say a Best Craftsmanship Plasma pistol, you're looking at something incredibly bespoke and valuable, most likely ancient as well. Anything best craftsmanship almost certainly isn't made in bulk. That's for common, or sometimes good, craftsmanship. Doesn't seem the sort of thing you'd find in Crazy Al's Gun-o-ramma. I'd say you're more likely to buy it from a planetary noble house's collection or some Magos with the keys to the AdMech armory, than anything resembling a weapons shop.

Maybe the noble house is down on their luck and need money, maybe you can get them on a preferred client list for some high end rejuvinant treatments, or maybe you offer them a % stake in an off world shipping concern.

Maybe the Magos desires a piece of archaic data you've got squirreled away in your core cogitator stacks, or perhaps you can get a manufacturing contract switched from the Magos' rival to his manufactorum.

Or maybe the purchase is being made on some backwater (and the PC's made the roll despite the penalties). The plasma pistol originally belonged to a founding family of the colony, and they're selling it off so they can fund the finishing of a space pier so there's a place for ships to dock in system.

Etc etc.

1) No idea. Lure is a classic and stereotypical FFG module...brilliant idea, poor execution. There is so much in that single modulue that defies logic.

2) Core Book, p.270, Table 9-34. Don't make it rocket science.

3) Love/Hate. I love that book, I really do. There's just so much about it that's wrong...just wrong. It's arbitary. It's contrived. It's a railroad. But it's a beautiful idea. I completely redrew it for my current campaign. I redrew the mass combat rules, both for ground warfare and space warfare. I redrew the scale. After my players played through the first space battle, I asked them to play through it again. I wanted my new rules playtested further. I'm not happy with mine, so I can guess how FFG designers, writers, and playtesters felt about this module.

4) The Warpstorm Trilogy reminds me of another awesome failure in trilogy modules from back in the day...Bloodstone Pass, Bloodstone Mines, Bloodstone Wars. The parallels between the two are close and I'd be surprised if one of the main designers hadn't played those, or at least read through and was influence by them. They were D&D modules back when the switch was being made to the Forgotten Realms....that right, TO the Forgotten Realms...all you fanboys that retched when the switch was made FROM Forgotten Realms should remember that this wasn't the first time TSR/WotC/Hasbro or whoever owns it now has pushed the big red button. It was also the switch to AD&D and non-weapon proficiencies introduced by Oriental Adventures. The Bloodstone modules showcased the new Battlesystem rules for AD&D Mass Combat. The first module was one of those brilliant ideas/poor execution due to logic failure pieces of work while the second module was the craziest dungeon crawl ever (move over Tomb of Horrors)...and also had mass combat in it. They outdid their own dungeon crawl in the third module. I've gone on enough about it. It's a good read. I recommend it. The parallels are close enough that a good lesson in scenario design can be had right there. The plots are a straight rip from The Seven Samarai/The Magnificent Seven.

5)Straight from my roll20 House Rules...

Elite Advances
Elite Advances for Skills cost 300 XP. You can't purchase the +10 advance unless you're at Rank 4 or are willing to suffer 1d10 Insanity, and can't purchase +20 until Rank 7 or suffer the same fate. Elite Advances for Talents cost +100% XP. You can't purchase them at a rank earlier than their usual career can, unless you are of that career. You can reduce the XP cost to 150% if you are willing to pay 1d5 Corruption.

I have some additional caveats (e.g. some Forbidden Lores can't be taken without a decent in-game attempt at locating such info).

6) You kinda lost me in the acronyms. If you're asking about group-affecting Talents like Void Tactician, I let it operate for the whole ship. It's hardly the difference between hit and miss on a PC ship. It might be the difference between Crit and No Crit. I'm not a stickler on such things.

7) I'm not strict on personal gear. It seems a bit stingy to make it hard to get a BC plasma pistol when there's xenotech on the market. Anything can be had at my Footfall, but good luck finding a xenotech ship component anywhere else. I usually only let archeotech ship components be purchased at the Lathes, or my modifiers are tough. You find what you find when voyaging. To me the hard adjudication comes when they want to sell xenotech. Figuring out PF for sales is tough. Once again, ship components is easier since SP can be converted to PF easily enough, but what about a cargo hold full of Stryxis tech?

You've asked similar questions in the past. These must be your group's sticking points. Every group has them. Talk as a group. Most groups are mature enough to realize that if anything is given to them, that when fights get too easy, the fun factor decreases. I regularly talk to my group and pose them GM questions much like you've asked here. If I see it coming I ask ahead of time.