I'm not familiar with the current state of FLAC but as of a few years ago ALAC offered better meta-data in the MP4 container. Part of the reason I abandoned FLAC years ago was constant problems with meta-data. I would often end up corrupt files post-tagging or the player would simply not show meta-data I had meticulously added to my bootleg collection. I got the sense at the time that there was a lack of agreement on how meta-data was supposed to work in FLAC files.