It's not a problem per se: rF2 treats each skin as a different car, yes. You can have multiple liveries for a car. Not sure why it was made like this, as it gives problems when you have custom skins and then get an update to a car model for example. But that's by design...
Let's just say that the way rF2 handles (not just) FFB settings leaves a lot to be desired. Personally, I'm also kinda tired of having to re-adjust my FFB after every single car update.