Since the guy is an emergency caretaker, then he wont be used very often. I havent seen too many situations where an "emergency caretaker" was actually needed, so no I dont think the NT would be controlled by someone who wasnt elected for a long period of time.
This would actually allow for some type of "succession" plan with NT/U21 managers, choose someone who is interested in being the U21 or NT manager in the future and let them choose a lineup once or twice.
Also, I think if you vote for someone to be your countries NT/U21 manager then you have faith in their decisions, so you should have faith in the person they choose to be an assistant.