I have written a fast-PWM library for SAMD21G-based Arduinos, see:
It should also be available from the Library Manager in the Arduino IDE.
The library lets you use the SAMD21G's timers TCC0, TCC1, and TCC2 to generate PWM signals on up to eight pins, with adjustable frequencies and resolutions, and gives you 96MHz to play with (so a 1MHz PWM frequency at a resolution of 96, 384KHz at a resolution of 250, 96KHz at a resolution of 1000, etc.)
Use, test, or comment as you see fit.