beaTunes closely works together with iTunes to create playlists. I do not believe it uses the nero layout format. Can you repro the issue with the m4a that I shared? Is there any way to debug using the files what can be the cause?
There is a known issue with nero tags.
You have a certain work environment that leads to you reporting a bug.
I would say that right now it is up to you to show that this is a completely new case.
I think that such reports are marked [AF]: awaiting feedback.
I would then conclude that the root cause is a not well documented (standardized) specification of how tags are used in MP4 files by Apple. What fixed it for me is running the dBpoweramp [ID Tag Update] Utility Codec to fix the tags. Any additional edits by beaTunes to the tags are fine and not causing any issues.
Use the dBpoweramp [ID Tag Update] Utility Codec to fix the tags
Run beaTunes analyze to sort out any tag issues and add the special tags to the files
mp3tag can read the tags fine now even after beaTunes edits the tags, while this was previously causing the issue.
It is probably a combination of factors. However mp3tag was the only tool that had problems to read the tags. Feel free to close this as Not a bug (By Design)