I think you may have misinterpreted the instructions - you need to have some sort of environment to run the makefile script included with the USBaspLoader bootloader fork. All of the settings are preconfigured for the Atmega32A and if you're familiar with building QMK and setting up MSYS2 (assuming you're on Windows) you can use mingw to build the .hex you need to flash.
I've attached mine (main.hex), although it did build with 1 error I failed to identify - my keyboard still works regardless of that though. Personally I would recommend using
https://github.com/zkemble/AVRDUDESS to flash the microcontroller
Note that you will also have to burn fuses which you can find in the Makefile.inc, but note that you will no longer be able to flash through the Arduino as ISP without the external crystal attached to the XTAL pins of the microcontroller once you've done this. For reference, they're as follows (formatted for avrdude(ss)):
-U lfuse:w:0x1f:m
-U hfuse:w:0xc0:m
I've also attached my build of the default .hex for the Discipline from QMK, in the event that you're having issues setting up MSYS2 and the required repositories.