The Apple IIGS only has 64k sound memory, and NinjaTracker has to fit all instruments in there. Even worse, instruments need to be placed at certain memory boundaries, which may reduce memory even further.
Also, at the end of every instruments, 8 stopper bytes are added.
This results in the following boundaries for instrument sizes:
So for instance, if a MOD instrument/loop header or loop is 2050 bytes, its boundary is 4088, and potentially wastes a lot of memory. In this case, it would be sensible to try and reduce the size to 2040 bytes.
The converter will give hints on how to tweak the MOD instruments.