I'd be interested to hear if FLAC through android auto sounds better than a high quality MP3 through USB.
I have the same MP3 files on my phone as on my USB stick, but never did a sound comparison.
I will say that sometimes Android auto is a pain to use, so you might want to convert your FLAC files to MP3 just to have the option of playing them through the USB interface.
I much prefer the HU's nav to anything AA provides.
I'm coming from more than a decade of using TomTom devices, which are, imnsho, the best navigation units out there. Their user interface aside (not great anymore), their navigation is the
best. Garmin is a distant second.
Waze and GMaps are awful. Terrible UI's. Always giving 3 routes, and never picking the best one. Zero customisation. Terrible handling of custom POI's or saves. Plus, GMaps tracks everywhere you go. I'm a privacy nut, so that's a strike against for me. They're awful.
Otoh, I use PowerAmp (Pro) for listening to music on my phone, and the AA interface it comes up with it actually really good, so I'm kind torn.
All-in-all, I think the HU's nav and audio "just work", and AA is a really bad overlay and provides very, very little for me, since I dont use streaming services like Play Music or Spotify.
Either way, if I want to listen to something from the hard drive, its trivial to convert FLAC to MP3 if I really want something on there.