This does already exist? There's Hegemony painted Wolves and Lashers. I think every faction has it's own paint job of the Buffalo. The Pirates have their own Hound and Mule. There's going to be more pain jobs, but those are some of the ones that already exist.
Technically they exist, but each and every one of them is manually created, presumably manually painted (Would have to see if the files use an extra layer that differs, which would be sane) and hence only a handful of ships which are manually set to be supported are able to be treated like this. The ships are apparently identical, but each variant is an entirely different ship, same as the disabled variants. Hence, each one shows up in the codex seperately, flooding it with yet more ships. Also, as no link between the ships exist, it would be unfeasible to actually paint them or whatever.
While technically functional for, I guess factional differentiation, it is a painfully bad implementation. Its the kind of thing you would do if you were modding another game, and since it didn't support different unit appearances, you had to use two units.
Back when I was modding Warcraft 3, I ran into issues with trying to let buildings construct more than 11 types of structures. I had to add a dummy-transformation ability which was script-supported to replace the builder with another builder with a different set of structures it could build, since the command card limited you to 11 structures, and there were around 40 of them that needed to be available. Hence, the excessive workaround.
Here, this is an actual game, and being developed by someone who actually has full access to all the code, as opposed to data and lesser script manipulation. A lot of things that are hardcoded for modders are not for the actual developers, so such an implementation is somewhat painful to see.
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Make the base varient of each ship.
Add alpha channels (I think that's the term for partly transparent parts of a model) to any ships that should support painting. Allow some method in refitting to alter the color layer underneath, which matches the faction's color(s), the player's color, or allow the player to chose the color as wanted.
Degraded variants should have in-built broken-weapons(Like onslaught, but does nothing) and in-built hull mods(As current), which are part of the varient extention instead of the base ship definition, and possibly a alternate graphics model.
Degraded variants could be visible from an extra tab in the codex. As a varient of the base ship, functionality to support repairing would be possible.