Right now my tagger can only embed one cover for the whole discset, although each disc has a different character, a different kind of tracks (first is backing, second theme songs, third additional unreleased tracks) and a different cover.
This has been a known issue for years. AFAIK it’s mainly an issue with Picard; it’s possible to use the comment box to denote which cover belongs to what medium or so forth, but Picard is not able to process that information.
I’m not sure there’s a ticket for tracking per-track cover art, but there is one requesting cover art on recordings (and not just releases), which I guess is kind of related: https://tickets.musicbrainz.org/browse/CAA-74
Don’t know how well this would work, since some people will write “Disc n”, some “CD n”, some “Medium n” and maybe it’s just because the comments contain the words.
Cover art does have an order stored in musicbrainz.
If there is a second image marked as medium or front cover for example you could assume it belongs to the second medium and write it to the file.