The AT90PWMxxx chips was designed for dimmable ballasts, and as far as I have heard, this is not a problem in that application. The dithering is used to change the frequency, and not the duty cycle.
The requirement is that you should be able to change the average frequency by 50 Hz at an 80 kHz pulse frequency. The lowest frequency is then 80 kHz / 16 = 5 kHz, and this is much faster than what an eye can detect.
Best Regards Ulf Samuelsson