Hi @owen-bern
One issue with using an external, auxiliary microcontroller, is that the flight controller itself is a self-contained, closed loop control system. This means that the flight controller will do everything in its power to maintain the aircraft orientation commanded by the pilot.
Anything outside that closed system is simply an impediment to getting the aircraft from your current orientation or where you are now (sensor input), to your future desired orientation or where you want to be (pilot setpoint). The difference between the two is the error (setpoint - input), which drives the PID control loops that control the aircraft's motors and servos.
If you introduce another microcontroller thats managing aircraft control surfaces external to the closed loop, the flight controller will simply fight it, until either it overcomes the impediment to its motion (with the PID integral term), or loses control of the aircraft.