So, you sit down to build a ship. You pick your hull, get some bits, and then you start to flip through the archeotech and xenotech components. Obviously, some of these things are very cool; there might even be a few that I keep around as "mandatory will takes", if possible, only leaving them behind if I A. Don't have the points, or B. Am specifically told no. Is there any little, easy number for how many of these a ship should be able to have, assuming you don't find one in the void with more, since it's been drifting there since 126.M33? On the one hand, given time, money, and someone capable enough of finding them, I can see you getting lots of bits replaced with "older, better stuff", or "other people's stuff who did things different (better?)". Do you ever cap how many, or just say "make this as good as you can, because there are consequences for that, too."

As a side, and it's a bit dumb, how do you make xenotech work? I accept that your mandatory AdMech hangers-on will need new spark plugs if they get to see, or even USE something archeotech, especially OLD archeotech, but xenotech? That's tech-heresy to them. If you return to the Imperium, say to go to Scintilla, for any reason, will they get pissy? I am aware that the Warrant of Trade lets a Rogue Trader do certain things others can't, though I like to assume many of those are contingent on them having the good decency to do so in someone else's (read: not the Imperium's) lawn. If you fly your ship in, sporting Eldar solar sails, since they are external, at least, can you get in trouble, or will your paper cover everything? Can the AdMech of a facility, say the Lathes, or above Scintilla, refuse to assist your "polluted" vessel, or is your money just good enough? The chance to study that "alien garbage" that they can't surpass too good an opportunity to pass on? I can imagine your Explorator got the job because of their drive to learn about "out there", but I doubt that means they, or certainly your ship's other Tech-Priests, might not throw a fit when you request they set up, or maintain, your Shadowfield Generator. Has this ever been an issue in a game you've played?

Last bit. If your ship has one of a few starting pachkages/backgrounds, it gets to start with one of these components, be it ATech or XTech. Can you come up with a good reason why? If you went to a ship yard, or the Breaking Yards, why would they leave that part in there? Pull it out, and make someone have to pay for it, and just it, either to make a profit, or just to sell it, because how many people show up for a whole, kitted ship? If you got it from your parent/predecessor, sure, but if the story is "you are the first Dynast", it seems weird that they left a very expensive part in there, vaguely like when I got my PSP, and the pawn shop dealer only then realized that there was a memory stick in it, that he otherwise would have charged me more for.

With the system as is, certain components are no brainers for effectiveness for their cost. Logically, some of these should have higher SP costs or be harder to find to represent the inevitable demand for them.

The Ad Mech have been known to install xenotech on their own explorator vessels to test it, look up the explorator fleet pdf for Battlefleet Gothic. A rogue trader vessel is even more expendable in comparison and they have the legal right to use such things. Some factions of the Mechanicus actively experiment with xenotech, believing it to be a source of valid knowledge. And sometimes a ship comes with components that cannot be safely removed. May as well use the otherwise worthy ship, and certain rogue traders are willing to do so.

Rogue Traders are regarded as a bit weird, but tend to be very rich and very well connected, so only a very foolish Imperial would assault that ship without seriously good reason. A few odd components likely won't cut it, unless they are glowing with warp energy.

Archaeotech and xenotech don't come with labels showing how expensive they are. Unless someone knows what they're looking for, it's simply another weird component. And even if they did, who's to say that in game, that single component didn't account for a significant percentage of that ship's cost? Remember, this is equivalent to profit factor being lost, not acquisitions.