That should be correct: ScummVM expects the audio tracks to be numbered 1 and upwards, even though I guess technically track 1 on the CD is the data track.
With the caveat that I've never played the game on a real FM Towns, nor in an FM Towns emulator, I don't think track 1 (and its alternative form, track 9) are played at all in the FM Towns version. In the EGA version, that tune is used for the Roland MT-32 overture but the FM Towns doesn't seem to have that. (It's no big loss, since it's pretty much just a black screen with the word "OVERTURE".) The tune is also used in the TurboGrafx-16 version, but as a replacement for another tune. It's strange.
The second audio track is what's used for the intro, and sounds similar to what the EGA and VGA versions use.
The table in the Loom wiki page "accidentally" documents what the FM Towns audio tracks are used for. Well, almost. It turns out that some short musical stings that the EGA version uses for certain dramatic scenes (and that are essentially lifted from longer tracks) aren't played in the FM Towns version.