It's good you found out that decompressed FLACs are bit perfect compared with WAVs (it's in the name 'FLAC'). You can fit roughly twice as many FLACs onto a given USB stick.
You probably already use MP3Tag to bulk edit tags and cover art (i.e. the metadata) for the FLACs, but if not, try it, it's excellent, especially if you set up some "actions" and "tools" to automate it. I have very many FLACs ripped onto my NAS, and all have been meticulously processed using MP3Tag, AlbumCoverArt, and Foobar2000 (for ReplayGain tagging) - the file tags are completely uniform and contain all the data of interest to me, and none that I don't care about. Looks great on the display screen of my amp, or on the control app on my tablet and phone.... Maybe Volumio does all this automatically, but you mentioned inconsistency - "Hmm, why do only some of my songs have correct meta data...?".
Yes - I'm a bit OCD and "on the spectrum"!
Sorry - I'm wandering off-topic!