If a board currently supported in QMK uses a Pro Micro (or compatible board) and you want to use the Proton C, you can generate the firmware by appending CONVERT_TO_PROTON_C=yes (or CTPC=yes) to your make argument, like this:
make 40percentclub/mf68:default CTPC=yes
You can add the same argument to your keymap's rules.mk, which will accomplish the same thing.
This exposes the CONVERT_TO_PROTON_C flag that you can use in your code with #ifdefs, like this:
#ifdef CONVERT_TO_PROTON_C
// Proton C code
#else
// Pro Micro code
#endif
Before being able to compile, you may get some errors about PORTB/DDRB, etc not being defined, so you'll need to convert the keyboard's code to use the GPIO Controls that will work for both ARM and AVR. This shouldn't affect the AVR builds at all.
The Proton C only has one on-board LED (C13), and by default, the TXLED (D5) is mapped to it. If you want the RXLED (B0) mapped to it instead, add this like to your config.h:
#define CONVERT_TO_PROTON_C_RXLED