Well, at least humanity still exists 10000 years later.

So, warp gates, and entrances to the warp are a thing, I accept, but why can't the way into the Webway just be closed? The Grey Knights and Ordo Malleus are supposed to be very good at this sort of thing, and while I accept that they can't just set up several null rods, which would harm the Emperor's mummy, it just seems ridiculous that, where once there was no door, and now there is, that it can't be shut, or broken, and forced to stay shut. it's a nice caveat to keep the Emperor where He is, and important, but it just doesn't seem impossible to fix, especially for such experts in those things.

I always viewed the daemon golden throne thing as just another grim dark silliness to toss on the silly pile. It's just another reason to point to the Emperor dying being very bad. Something that seemed cool for one book that affected the setting, but didn't openly conflict with anything. Something I generally ignore or don't consider part of my what passes for my personal fairly inclusive canon(Bloodtide never happened).

Actually. A Death Watch game where you played Grey Knights entering that portion of the webway, and trying to either seal the hole, or turn off the inside power source to close the entrance to the palace sounds kinda badass. Like you would be briefed that the Empra was dying, and you the greatest of the great Battle Brothers had to go on the single most important mission ever. To neutralize the webway portal by any means necessary. So then like, you're walking in the throne room with the Adeptus Custodes, gazing upon the throne, manly tears. Super high level toons, all psykers, optimal load outs, tons of punching greater daemons in the face! Oh man, it's great!

Besides running a game with that as the premise, it's a meh idea I mostly ignore.

So, warp gates, and entrances to the warp are a thing, I accept, but why can't the way into the Webway just be closed? The Grey Knights and Ordo Malleus are supposed to be very good at this sort of thing, and while I accept that they can't just set up several null rods, which would harm the Emperor's mummy, it just seems ridiculous that, where once there was no door, and now there is, that it can't be shut, or broken, and forced to stay shut. it's a nice caveat to keep the Emperor where He is, and important, but it just doesn't seem impossible to fix, especially for such experts in those things.

Various reasons, but these are my answers to your questions.

1) Null Rods only affect a short range, and they really only work inside the Materium. The Golden Webway is actually inside of the Warp, where rules don't work the way things do here. Daemons might be weakened, but they likely won't be completely destroyed. Or they can just throw a horde of the bones of the fallen at you. Or pick up a shard of Wraithbone and shank ya with it.

2) There were no experts in it, and there certainly aren't now. The Emperor played this one really close to the chest, and most of the personnel on it were killed when Magnus whined hard enough to rupture the time-space continuum.

3) I assume the problem here is that the Emperor didn't create a tunnel or a hole into the Warp, he tried to open an actual conduit that would lead into the Webway, essentially attempting to replicate the technology of the Old Ones from scratch. He likely didn't have perfect knowledge, and now there's a permanent link between Terra and the Warp.

The daemon throne is somewhat new, but the Emperor used to just be some guy, and Horus used to just be some general. I think it actually makes sense, and I'm a fan of it because it's yet another reason why it would suck to live in 40K times.

how much XP do you get for killing the Emperor?

When running RT...or any game...stick to the script the your first time out, and probably your fourth or fifth. For most games, give the players a concrete starting objective that is currently beyond their capability (slay the dragon, awaken the sleeping princess, avenge your father's death). Then, give the players a series of adventures that force them to travel, grow as individuals, and gel as a group. Give them time to develop their characters' personalities.

In RT, give them pirates to fight, ancient ruins to explore, xenos to confuse them, rivals to confound their plans, and a background war that threatens to overwhelm all their well-laid plans. When everything comes together your players will know it and they will tell you it's time...no need to make this stuff up. Then let them achieve their original objective, or at least take a shot at it. If they fail, maybe they go back to square one and try again. If they succeed, game over, start another. Fu was had by everyone.

If you have to ask complete strangers what to do with your plot, then your story is out of control; it isn't your story any more. When you've run a few vanilla campaigns you won't need to ask anyone's advice on plot, just rules clarifications, or ideas on challenges or rewards. It's sometimes hard to come up with new and exciting monsters and treasures, not to mention dungeon crawls. There's nothing wrong with vanilla campaigns. My most enjoyable long-term games started very vanilla. I'm sure most long-time players and GMs would concur. It's those games that start vanilla and turn into something else by player design that really last. When the GM forces it, it usually spirals out of control and crashes.

On the other hand, free story games are just as fun, even more so, although they're much harder to pull off on the GM side sadly.

The most fun games I've been apart of, as both player and GM have been the games where the players wrote the story. Pretty much the GM just set the 'game board' (you start in this place, stuff X, Y and Z is happening, it's up to the players how they mix themselves into the world events). They do require a certain kind of GM, capable to do a lot of thinking on their feet, since in this kind of campaigns most of the time is spent adjudicating the world's reaction to largely unforeseen player action.

The classical 'world does stuff, players react to it' is a lot easier to run than 'players do stuff, world reacts'.

That being said, IMO pretty much the worst thing one can do as a GM is having world-changing events happen as a cutscene and/or background events (unless that was the whole campaign premise, explained to the players beforehand).

Killing the Emperor and exploring the consequences is totally cool to to if the players decide to attempt it and manage to bypass all the obstacles and pull this off (the last game I was in was heading in that direction at some point, but ended up with a Rogue Trader/Inquisitor, together with Vulkan and Girlyman seceding most of Ultima Segmentum from the Imperium as a new Empire, friendly to the Tau).

It is an entirely different thing to show up to play 40k and, few sessions in to find out 'btw, a NPC killed the Emperor and everything is upside down now'.

Fair point.