It's a good point ...and I just did such an install today!
That's exactly what the instructions specified; and the way the cord exited the microwave, I defy anyone to do it otherwise.
Yet, that does seem to conflict with the NEC rule against passing cords through walls or partitions. Perhaps - and I'm just guessing here - it's allowed here simply because the receptacle is still readily accessible. Such is not the case where the receptacle is in another room.
As such, though, I'd insist the hole be large enough for the plug to pass through.
