I'm a bit confused by this, so essentially you are proposing removing all skill and upgrade choice from players and forcing them to use presets, which can be purchased for real $$??
To be honest all it seems this does is reduce variety and lock playstyles behind a paywall.
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.