Story points shouldn't be spent to build in hull mods at all
This gameplay change only revealed an inherent problem with hull mods - you are fighting for weapon/venting/shield slots and 99% of the time the cost isn't worth it.
All I'm doing now is building in heavy armor, hardened shields, and integrated targeting on every ship because those are the most expensive and most useful.
Then, I don't even bother with other hull mods because they do next to nothing worthwhile compared to their OP cost.
I would prefer an alternative system where hull mods take up their own slots, and hull mod slots are available on a case-by-case basis but generally with low-tech favoring lots of hull mod slots, and high tech favoring very few.
So for example, a low tech ship may have 6 slots to work with, a midtech may have 4, and a high tech may have 2.
Rather than paying an OP price for each hull mod, you can just put whatever hull mod you want.
This will typically mean that high tech ships are getting integrated targeting and maybe hardened shields, while a low tech ship would have integrated targeting, hardened shields, heavy armor, safety overrides, flux vents, etc...
This means high tech ships tend to be more specialized, low tech more do everything.
I'd take this a step further and get rid of most hull mods that are simply increasing shields, adding damage, adding range, etc. We need more interesting things than stat buffs.
That's my 2 cents on it anyway. Whatever it may be, I just don't think the current system of paying OP for hull mods works and the above is just one idea to try and get away from that.