Let's say a fighter were to have a stance like Stephen Thompson with feet facing horizontal to the opponent and the opponent threw a high kick and it hits the back of the head but knocks him out. Do you think the back of the head rule would even come into effect? 
No.. The rules seem to not matter as much in the standup. Technically GSP got hit in the back of the head but it wasn't a no contest or anything. It just happens. You don't know what your opponent is going to do when standing or where they will be moving. At least on the ground and you're on top of them, you control their movement a little more, making is easier to predict where the back of their head could be.
I don't think so. There's so much movement in stand up that a variety of factors could cause the kick to land on the back of the head.
Thanks for the clarification