That is another aspect which can be very cumbersome indeed. I understood your first comment to be about differences in the data of the same audio file which various scrobblers submit to LB. How LB goes about picking the right MBID from various identically named recordings in the database is another can of worms. The problems you mention for different performances of the same classical piece also plague live performances of popsongs. A similar problem that I often encounter is that LB maps recordings of dance classics to DJ-mixed versions in the database.
If only all scrobblers submitted the MBID, this could be solved.