It looks like all my multi-disc albums that are complete and have all track and disc numbers still return N when they should return Y on Album Complete. Not 100% sure, but the most likely culprit seems to be that all tracks are numbered consecutively, like 1-32 instead of 1-16 and 1-16 (but discs are still numbered, too).
Tangentially related, changes that affect Album Complete don't seem to apply properly until you restart MusicBee.