Spend some more time on MusicBrainz Picard. Once I got all the scripting straight, there was no reason to use any other Tagging program, unless the release wasn't in MusicBrainz, and I had to revert to Discogs. Once you embrace the MusicBrainz system, everything else falls into place.
I believe all of your issues are solvable through scripting, or a more thorough understanding of what MusicBrainz is and does. I found that most of my problems were my own creation, because I didn't understand the metadata, or I scripted badly. The genres are a nightmare, but no one has those figured out canonically. I think I finally settled on Artist genre, or only the top genre per song. Anything more than that, and it becomes just about useless.
You might also check into some other apps like TagScanner, and kid3 to make sure you aren't dealing with residual tags from the original source. Might also be issues with the difference between APE, ID3, and Vorbis, depending on your source files.
Dell Inspiron, i5, 16GB, 256GBSSD
Windows 11 Preview
MusicBee 3.4.7735, installed on C:\
Library on External drive;
267,193 Tracks, 16,859 Albums, 3794.19GB, 774d 16:09
[font=Roboto, "Segoe UI", sans-serif]Topping D10 32bit 384 kHz USB DAC[/font]
O2 Headphone Amplifier
beyerdynamic DT770M 80 ohm