OK, now I see it's MODPlug Tracker who inserts silence I actually know nothing of mod music, you understand, but just write my songs in the only editor I know how to use - Guitar Pro - and then export them. Unfortunately, it can only export them to MIDI or WAV. I don't like the idea of a single song being bigger than the rest of resources combined, so I think WAV (and even OGG) is probably out of question. And Allegro does not play MIDI now So I used MPTracker to convert MIDI file into IT file (convoluted way, I know).
Now, I think, I can try to write a MIDI addon for Allegro (which many people asked for anyway) or use big-ass OGG-files (although, with carefully chosen compression options they might be not so big, probably).