This seems to be related How Do Star Ratings Work Across Multiple Song Of The Same Artist?
Update: Upon further investigation this behavior does seem to stem from the fact that all affected tracks possess the same “Recording ID”, a relationship which is described here. I believe the Plex GUIDs should be based on the track ids.
In fact, both MusicBrainz Picard and mutagen seem to map the musicbrainz_recordingid to track id for various formats. In Picard’s case, this seems to definitely be intentional, so it’s likely that mutagen followed their example - unfortunately this leads to really strange behavior in Plex, and I’m really not sure what the best solution would be; perhaps some sort of toggle that tells the scanner/agent to prefer the real musicbrainz_trackid instead?