I have the same issue, with my FLAC albums in a separate folder on my NAS, and that means I can’t/don’t listen to the FLAC versions on the Pi. (If I add the FLAC folder to Volumio, and if I have both MP3 and FLAC versions, I’ll see the same song twice in the Volumio library… but I have no idea which is which.)
Ideal solution would be for Volumio to have the option to group FLAC albums/songs separately in the library web UI. Perhaps based on the file type; mp3, flac, aac, mp4? Or maybe based on the flag type; ID3, Vorbis? Dunno if that’s feasible?