Athiest people who claim they definitely know how the universe works

The thing is that atheists don’t do that. They are aware how science works and that what we consider to be true is only the current best approximation.

disproven by Godel’s Incompleteness Theorem

I don’t know much about most of the fancy words you’re throwing around. But I do know that the Incompleteness Theorem only states that statements can exist that you can neither prove nor deny. We could assume that a deity exists that chooses to hide its existence. This assumption would be such an independent axiom. If we take it to be true, however, then it is subject to reasoning, and we can quickly derive that this deity does not have the properties we usually associate with it. So while a deity may exist, it certainly isn’t the one we’re picturing, from which “God doesn‘t exist” follows necessarily.

It’s also worth noting that Gödel was talking about an axiomatization of mathematics, not the ‘real world.’