I like to use a different prescaler for Timer0 because I need 6 PWM outputs on a high frequency to control two stepper motors with microsteps.

I created a solution myself. The only thing I had to do was changing wiring.c to make calculations using the actual settings of the configuration registers instead of the defined default values.

See: https://github.com/GewoonGijs/platformio-pkg-framework-arduinoavr/blob/master/cores/arduino/wiring.c