As far as I know, the GUI has a max of 3 layers (base layer + two more), and with the setup I'd like to run I need at least 6, preferably more, which is why I'd like to use something like tmk's.
It also allows me to use functions, and in that sense it allows me to do actual programming for the keyboard (like a compose key feature directly on the keyboard without the need for software, or layout hotswapping between qwerty and dvorak, or even a virtual dip-switch), basically an unlimited amount of customizability.
If the controller is indeed an ATMega32u4 and I can flash a different bootloader that would be great, and I'd most likely purchase at least one PCB.
Now I understand why you want TMK, when I started in this mech boards hobby I wanted that too, now I don't even use macro's. I have one layout that I want on all my 60%, the exact same one, program the board once and that's it. I like simple things and I like when I change from one board to the other to expect the same behavior
But I understand why you want to do all that stuff, I can double check at home on my NerD60 PCB what is the exact part number on the controller. In order to flash a new bootloader you will have to figure out where the headers for the ISP programmer are located on the PCB, do the flashing with the risk on bricking the board and finally reverse engineer the matrix on the PCB, that is yet another sisyphean task, because if you don't know how the matrix is you will not be able to use TMK.
The best way would be to wait for the GH60 it works out of the box with TMK, it was designed for TMK. Or biuld a keyboard from scratch, plate mounted switches, handwired matrix and a Teensy or Teensy Clone here is such a board
http://deskthority.net/workshop-f7/brownfox-step-by-step-t6050.html
