You can just as easily get a USB-C dongle that would let you hook it up, or a bluetooth dongle or FM transmitter (my personal choice when I still had my 2010 Corolla), or, hell, even a new head unit that'd support it natively. I have plenty of friends who've gone that route. You could leave it in the car. They're not dear enough to prompt a thief to get in just for it. And you can get other, admittedly more bulky ones, that also allow you to charge your phone while it's plugged into aux.
Seeing FLACs isn't a thing that a phone can individually decide or not, it's 100% about the app you use. VLC will see them fine, my personal music player of choice for local files was Poweramp when I was on Android last, and even your pack-in music player should very well also see and play FLACs fine though it might have some stipulations the other apps don't regarding bitrate, sample rate or bit depth.