Steven: I tried removing the Artist and Title tags from a FLAC file in my library using an external tagger, and rescanned it in MB. Then, did the manual auto-tag by track option/identify track and update tags, with "identify track title and artist using the digital sound signature" checked. The FLAC was found and the track/artist successfully added. So I guess in the case of FLAC format at least, it is working. The track though was not unusual/esoteric. FWIW.
Update: ditto for OPUS with a common title--identified/updated successfully with fpcalc.