Throttle based dynamic Notch filter when throttle is not controlled through Arducopter motor servo functions

I am controlling a quadrotor using a custom controller by sending PWM signals directly to the motors via pymavlink. Since sending PWM signal through pymavlink only works if the servo function is not assigned by Arducopter (i.e., has to be other than motor 1, motor 2, etc …), Is it possible to use throttle based dynamic notch filter in that scenario? If so, which servo function does Arducopter use to deduce the throttle?