If I understand correctly, fat16lib's approach is run Chibios/RT scheduler with the Arduino Due existing Library. That said, to control the hardware register, you have to use the Arduino library (writing pins, USB, timer, etc), not the Chibios/RT.
While what I am doing is implementing the low level driver for Due on Chibios/RT. No dependency on the Arduino stack - which means instead of digitalWrite, one have to code in Chibios/RT style.