Quirrel stopped the polyjuice spell to be intimidating, same as how he was manipulating the lights. Misdirecting the Aurors to polyjuice makes them more worried, and about the wrong thing.

But I think really it doesn't matter, because the reason in my mind why Voldemort isn't on Quirrel's head is because that would be fucking stupid. Plenty of changes from canon are simply people getting smarter, and this is one really obvious one. If his face HAS to be sticking out of whoever's body he is riding, the back of the head is basically the worst place to put it. It's way easier to accidentally reveal than say, the back, the stomach, or the side of the leg, and all of those places are covered as a matter of course by wizard's robes.