Hi there.
SVU3 and STFR dev here.
I'd like to start off by saying this is an AMAZING concept you got here. You've done great work already.
Now, regarding the ability to clean off cars...

You could theoretically replace the rust texture, which, if done right, would make supporting modded cars far easier.
If you do go down this path, you could make a timed action or some other form of interacting with the vehicle, that upon completion, removes all rust. You'd also have to make code to make the cars spawn with rust.

Another theoretical method would involve the "SkinIndex", where you'd use lua to add the worn skins to the vehicles without overriding the scripts, and then force the worn down skins when the vehicle spawns. Changing the skinIndex to the non-worn down skins when the cleaning action completes.

Do note the above 2 wouldn't exactly play nicely with wheels without a bit of lua finaggling.

The below does work out of the box with new wheels, as long as you define the new wheel textures as new wheel types, and make the new vehicleIDs use them.

An excessively complicated method of cleaning cars could involve making entirely new vehicle IDs that are copies of the originals, but just covered in moss and rust. You'd then use the new B42 only feature found in "ProfessionVehicles.lua" to automatically replace all supported cars when they spawn. Then make an interaction to remove the rust, and have the code replace the worn down vehicle with the new one on completion.

I've never personally dealt with making timed actions, nor new vehicle interactions.
BUT I would gladly help as best as I can with the SkinIndex/RustTexture/NewScript stuff?