Came across this and on the forums [1] Aerozol suggested that I should open a ticket about it.

Basically, it seems that on (at least) m4a files, the itunsmpb tag is used to store data required for gapless playback. By default picard removes this tag when tagging m4a files.

That's obviously undesirable so it seems that it might be a good idea to not remove this tag by default when tagging m4a files. Now I'm not an expert on m4a or tags by any means, but in mp3s for example, that information isn't even exposed to the user so my first thought is that that might be the best approach here as well.

[1] https://community.metabrainz.org/t/saving-tags-in-picard-appears-to-alter-the-audio-stream/622674