SPI Input/Output instead of PWM Input/Output

Hi
I made a DYI radio control with an nrf28lp transducer module to control my drone, I have to add an extra processing unit to convert data to PWM signal which is needed for my Ardupilot board
I was wondering if can disable all PWM Input/Output of board and deliver all Input/Output data in SPI binary string in each pulse cycle?
is there any concern in both Ardupilot hardware-software point of view when all Input/Output PWM be disabled?