ATmega - magnitude comparator for hardware PWM
The ATmega datasheet says on p. 128:

16.7  Output Compare Units
The 16-bit comparator continuously compares TCNT1 with the Output Compare Register (OCR1x).
If TCNT equals OCR1x the comparator signals a match.

It says the same about the ouput compare unit for the 8 Bit TCNT0.
So I would strongly assume that for simplicity reasons only an identity comparator is used. It only checks if all bits are equal. A magnitude comparator would be overkill.