In the current MatrixPilot versions, there is a special trigger action capacity connectable to output pin 6.
// Trigger Action
// Use the trigger to do things like drop an item at a certain waypoint, or take a photo every
// N seconds during certain waypoint legs.
"
Consequently, the PWM frequency and duty cycles are defined before the compilation and cannot be changed dynamically during the flight.
You will find more explanations in the config | options.h file.
If you want to command a passive buzzer at different tones and pitches you need to implement a special procedure to do that.
You can use, for example, two dedicated inputs to control the tone and the pitch (that you can include in libUDB | radioIn.c)
and a dedicated function to output the signal to the buzzer on output6 (that you can include in libUDB | servoOut.c or MatrixPilot | behavior.c).
See Microchip AN655 to have a typical example and asm code for sine generator using digital outputs.
I believe that is the only method to achieve what you are looking for.