The phrase "quality of FLAC" can be thought of in different ways. As far as audio quality, there is only one, and that is the same quality that was stored in the original WAV file on the CD. FLAC compression only makes the computer file smaller, no information is thrown away as it is with MP3s. The different levels of FLAC compression have to do with how small the file is made and how long it takes to do it. I only recently became aware of all that thanks to a post by Mark Fishman.
My experience as been that not all cars play FLAC files. In fact, I suspect that it might be rather rare. I'm hoping that would be changing as time goes by. For now, you'll have to check with either the dealer or manufacturer about any specific vehicle you're interested in. Unfortunately, there are dealer sales people who don't know what FLAC is, so they could tell you most anything. If you're serious about a particular car, give it a try - have the salesguy show you how.