After a year of searching I finally figure out a solution to my sound check volume issues. When I had originally migrated to apple music I uploaded my 20k song mp3 collection. It turns out it matched about 85% of it, but the other songs were just uploaded. Those uploaded songs do not work with sound check, they have to be added via apple music or matched.
So I've slowly been deleting my uploaded songs and replacing them with apple music versions. It's a pretty manual process and a PITA, but at least it should be fixed for 95% of my music when done. It's typically soundtracks and singles that don't match the exact album info in apple music. The other songs aren't on apple music at all (more indie stuff). I may test adjusting the track gain on the local mp3 and re-uploading it - not sure if that translates to volume level on cloud playback or only local device playback.
Hopefully this will help someone else out there.