Well. there's the -I|--intelligent-sort option that will make "The Beatles" sort as "Beatles". But sorting is always alphabetic, based on the directory or file name. Mp3tofid makes no assumption on the meaning of the directory depth. One level may be artists and the next level albums, but for mp3tofid these are just directories.
You could create a tree of symlinks like
/linksdir/Beatles, The/1966 Revolver -> /realdir/The Beatles/Revolver
and scan both directories.
Your music would appear twice, once in the order you like, and again in the order you dislike.
Pim