After doing some more searches and experimentation I now understand how things work, and have a solution too!
The sort order of tracks on the phatbox is based on the .idx files on the DMS, which are in turn generated from the .db files, and these are all done by PMM. So, the solution is to fix the .db files and to regenerate the .idx files from them.
I found a Linux shell script called
phatSort (written by "Cowboy" Ben Alman) that did this, but I massaged it further to make it work the way I like it. Now I have completely solved the "various artists" sort problem. When browsing by album, all albums are sorted in alphabetical order (and using the alpha seek, a cinch to find), and all tracks are played in the proper order. Yay!
My own version of the phatsort script adds more error checking, backs up the original .db and .idx files before proceeding, does some cleanup, and has minor tweaks to the sorting. Of course, if you want to use it you will need to connect the cradle to a Linux box, and you will need to re-run the script after each PMM sync/save/eject operation by PMM because the .db and .idx files will get mangled again. One other thing, don't forget to add "album_seek=alpha" in your Profile.ini to enable alpha seeking in album mode.