The Unique upgrades are locked at the very end. You can see all of them if you go into offline mode.
Heres a rundown of all of them:
(Pause to read)
Chaos has by far the most varied and extensive upgrade and Fleet scheme list, you just need to unlock it first
Best not to do anything mod related till the devs make it available, especially with EAC.
I just know a thing or too how the engine works.
Anything MP certiantly won't be made moddable by them, for the single player campaigns could be different however.
The devs system for assigning body and weapon parts is fairly straightforward,
And as you can see the Torpedo launcher is considered a separate entity to the prow (hence the gaps where the torps go).
From my tinkerings, it's 100% possible, but entirely up to the devs if they would consider spending time on it.
As far as collision box goes, it's pretty off for a lot of ships and isn't all that accurate to the model (thus I doubt it'd be a concern).
My suggestions would be:
-Either a slightly visualy customisable option as suggested here (via an unlock system)
-And/or unlock more Colour Schemes (like you unlock Race Portraits).
I have tested both, so they are possible.
Love that concept art btw, thank you for posting!
Ship parts CAN be mixed and matched (to a degree) via the json, so I would bet the devs could add the system. Would just take some artist time.
Different sections are assigned to different 'body locations' and are given co-ordinates relative to the ship base where they are to be located on the model.
As far as color schemes go, interestingly enough any factions color scheme can be applied to any ship (looks pretty dope!), so I could see unique color schemes being something that could be unlocked (or simply using ones from other factions).