It evolves toggling 1 pin at 408KHz and a second pin at 8.5Khz with specific timing and 50% duty cycle.
By the proper use of timers you can do this on an arduino, no need to go to an ARM chip.
I don't see much problems in powering a pin with 5 volt.
The point is that as the chip geometry gets smaller then a 5V system generates too much heat. The solution is to drop the voltage in order to not generate as much and stop the chip melting.
If you put 5V into a pin of a 3V3 processor then you will destroy it.
So setting 5 volt on the 5volt pin and 5 volt on the comparator pin would do,
Not 100% sure about what you are saying but no it would not do. The current arduino only has one comparator input the ARM chips do not have any.