The tracker modules not only are very powerful in optimal usage of space, but by nature they can re-use parts of their song for loops, and enable/disable channels.
Programming access to these channels would allow people to make a score which can easily blend from overworld to water themes, much like banjo kazooie did back at the N64. You fade out 2 channels, fade in 3 others. Presto! 1 file, two completely different tracks!
Obviously the alternative is to just have two files, but having two files with 90% of the instruments as a duplicate seems like such a waste, doesn't it? Besides, you get the overhead of this 2nd file running in order to fade over.