Ok, so far I've really only looked through xg.lgp, but I think it's safe to assume these two files are in the other MIDI datasets as well (ygm, AWE, and MIDI.lgp).
Yes, I'm well aware that comical.mid is unused, and that practically NOBODY has any idea why they kept it in there. That file, though, is not what I'm talking about.
It's these two files: "fin.mid" (file 33), and "oa.mid" (file 58).
Ok, the first one -- "fin.mid". It appears to be the musical score from the ending FMV, in MIDI format. As we know, the PC version has the score from the PSX version built-in to the audio track of the PC FMV version. So it begs the question: WHY? It's redundant! :P
Same thing with the first minute or so of "oa.mid", before it jumps into the bombing mission music. The first part of it is the MIDI version of the musical accompaniment of the opening FMV. Again, it's practically never used or heard in-game, though the latter part of it is -- it IS definitely the bombing music track file that is used in the beginning, as opposed to it just using ob.mid (which is just the bombing mission music -- this track, I believe, is used for the rest of the times in the game when this music plays).
I would imagine that the first part of oa.mid is actually played simultaneously with the FMV, just muted. Then, with some accurate timing, they fade in the already-playing MIDI file (via the program's internal volume control, I'm guessing), right as the FMV's backround music ends, giving you a nearly seemless transition from FMV audio track to in-game MIDI track.
Regardless, that still doesn't explain fin.mid's existance -- the song in its entirety is already part of the FMV's audio. So....any ideas?