Hey! This is 20 years thing! TK did it like that for the people who don't know how to program and flash on the PIC. So he created a MIDI bootloader.(Yes there's a bootloader ;)
During some times the PIC was sold with the BL already flashed, then there was no need of a programmer, only a MIDI interface was necessary cause the MIOS8 and the App layer are uploadable with the MIOS Studio, the .hex file! Which is sent as SysEx to the PIC.
I was a bit lost too at the beginning, without any ASM knowledge. But I tried, failed, succeed, and finally learnt a lot more than I expected.
Most of the people don't want to change a line in the code, they just want a working machine after have building it.
Conclusion if you want to change some lines in the code, you must be interested in mios8 and what it is.
Follow the procedures, try, after a few steps, you will see everything lights up. ;) BR
Bruno