Arduino: Generating time critical signals with interrupts
It's easy: you can't. And it's platform dependant.

Some microcontrollers have multi priorities interrupt controllers, so that if a low priority ISR is running and an higher interrupt is fired the micro stops servicing the low one, saves the context, services the high priority one and then gets back to the lower priority routine. For your example you would probably set the PWM to high priority and the buttons to low priority, waiting a handful of us for a human is not a big deal.

Generally speaking, if a micro controller does not have a priority enabled interrupt controller, an ISR is not interruptible. If a button gets pressed and after some clock cycles the timer wraps so it's time to toggle the PWM pin well... The pin will wait. The interrupt request bit is set and when the micro is done servicing the buttons he will return to the main routine and then go back to serve the new request. If more than one request occur while servicing another... That's platform dependant. There can be a fixed or programmable order, they can be served FCFS or maybe even randomly.

The key is: keep your ISRs short, and by short I mean short. The shorter, the better. Or, in this specific case, serve the not critical task by polling. You can have your nice while(1) and check the buttons inside there, and do whatever you need to do with your input, and generate PWM via interrupt.

And the final advise: don't use arduino. If you write all your code you know what it does and how it behaves. Atmel micros can be programmed in "vanilla" c or asm, and in my opinion that's way better.