I would like some insight on this and how it would work best, if it can work without breaking the game. As well, different builds that might be entertaining for this type of starship.
I can't proffer you a build without you specifying a BP amount, but there are a variety of ship's systems very compatible with your proposal. The most obvious is smuggler's compartments, which come with stock rules for being found, but you could also have the ship's computer "grow" based on roleplaying interactions with the party, perhaps indicating that it either likes them more now or has begrudgingly decided to help them more. *Most* systems are very hardware intensive, though, meaning that while the ship can refuse to use them (outside of passive always-on options, like armor), it'll be very hard to hide them from the players without improving the tech level of the ship to some extent.
Examples of that range from the very basic (the ship has retractable guns that only deploy when turned on) to the absurdly advanced and potentially OP (the ship has variable armor - you can tell it whether to have MKIV, MKVIII, MKXI, MKXIV, or MKXV armor, and it will reconfigure itself to obey you).
I think the BP system itself could be used to give you what you want. The ship just automatically upgrades itself as the characters gain levels. Instead of them taking it into port and upgrading it, the BP gain by APL is just them discovering new/better systems as they learn how to operate the ship. Maybe the ship comes with a learning AI and is made of nannites that actually upgrade the ship over time.
It could simply have broken systems that are going to require checks and resources that are simply outside of what the PCs can handle right now.
I think the BP system itself could be used to give you what you want. The ship just automatically upgrades itself as the characters gain levels. Instead of them taking it into port and upgrading it, the BP gain by APL is just them discovering new/better systems as they learn how to operate the ship. Maybe the ship comes with a learning AI and is made of nannites that actually upgrade the ship over time.
I'm a big fan of this concept, and it gives your PCs an interesting base of operations/home base that won't become outdated as the game progresses.
The same concept can also be applied to a PC's trademark piece of equipment/weapon/armor.
Sounds like a neat concept. One possibility would be having a living ship that grows alongside the characters (like Talyn from Farscape). Then the weapons/modules/defences being unlocked could be explained as them growing or as the ship learning to use them. There's even the medium sized Oma ship frame from Alien Archive, if you decide to go this route.
Another thought off the top of my head would be that all controls and consoles in the ship are encoded in either a strange language or encrypted, and the PCs have to figure out how to use them (either using culture checks with progressively higher DCs for more advanced modules, or using translations found during quests).
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I like the idea of the ship upgrading as they go. The only issue I can see with unlocking systems/upgrades automatically is that it removes choice from the players.
Perhaps whenever they get an upgrade unlocked the ship gives them a choice. Console lights up with three icons: a gun, a tool or a computer chip. They select one and get an appropriate upgrade. This could be explained as the ship being designed to train its crew, so they only get access to systems when they have demonstrated proficiency with the lesser versions.
If you don't care about it making sense in-game, then you can just get them to choose.
For weapons I'd either upgrade the actual weapon or unlock a new weapon mount they can then get a new weapon added to (which they can conveniently acquire by cashing in a favour, of course.)