For a bit of precedent, consider that the Plumeria, which is widely considered a highly effective ship design, is not only surprisingly effective for its size (which would require us to design a pointbuy system where the value of a ship is linked to something other than its size, or some other contortion no one has considered before), but also has a hot tub. We'd have to ask ourselves how many points a hot tub is worth when building a ship, or contrive a way to allocate space that provides enough wiggle room that no one will ask about the 5 tons of mass allocated to the room, the water, the machinery, and so on.
Or we could just accept that hot tubs are intergral to the Yamataian design philosophy, which as we know is inefficient because they can afford to be, and because we don't want them to blow everyone away by trying their hardest to optimize for combat efficiency, because then they just wouldn't be the Star Army anymore.
Every faction is supposed to do things differently. To maintain that with a pointbuy system we'd have to include rewards for designs that are otherwise suboptimal but fit factions, and penalties for making 'smart' decisions that go against a faction's philosophy. For example, Nepleslian ships that don't have excessive firepower, Freespacer ships that aren't deathtraps on the brink of destruction, or Yamataian ships that aren't clean and comfortable. And then designers would be trying not to overflow their penalty box while optimizing their ship against the base system, instead of trying to epitomize their faction's ideals.
That's after we somehow work out a detailed point-buy system that incorporates and balances everything I listed in the first paragraph of my previous post. All around, this doesn't seem like a good idea after all, does it?
We do need to write down what's acceptable, but it varies depending on what we're making, so a cohesive ship design system isn't the right way to do it.