Thanks for the advice. I'm going to look around, because you're right. It doesn't even keep the pitch bends when I tried copying and pasting the track from the non-MIDI version for the MIDI version. So I guess that's something to note for FLStudio users.
I did find out that you can make MIDIs in FLStudio through the mixer. The issue is that the mixer itself has to actually have the tracks aligned for what they are "mapped to in the mixer" rather than simply assigning the MIDI instrumentation for each track itself. Then for each Pattern that's the non-master Inserts, you have to assign instrumentation.
While it might not be useful for hacks, this means that you might actually be able to have each track change its instrumentation mid-song based on patterns. I don't know enough about musical insertion in GBA files, but I'm curious if you could swap instruments mid-song. Since you're not actually exceeding the amount of tracks allowed, but rather telling the track to play with a different instrument at a certain point.