Suppose, for the sake of argument, an Omnipotent Being that is independent of time and space, created the Universe and everything in it, which we observe today. Is the fact that humans do not understand how it happened, evidence that such a being does not exist?
Yes, it is.
It isn't very strong evidence; But it gets stronger each time we discover more accurate and detailed ways to describe the universe, without finding any hints whatsoever of the alleged omnipotent creator.
By the end of the twentieth century, it had become clear that we understand all of the interactions that are possible at scales relevant to humans, and still there's no hint of any gods - which rules out all the other major ideas of the people who hypothesised an omnipotent creator to begin with. That's pretty compelling evidence that their remaining idea isn't coming from a source worthy of our respect.
If some guy claims to have been kidnapped by aliens in a flying saucer, and we know that he has a long history of telling tall tales, and we have found zero evidence to support his claim, and the only people who are supporting his claim are those who supported his earlier false claims, then that's pretty good evidence that the aliens in flying saucers don't exist.
Even if aliens in flying saucers in fact DO exist, it would be foolish to believe that they do, based on the evidence before us in that scenario.
The evidence boils down to 'we cannot 100% definitely prove that this unevidenced speculation isn't true', which is the same level of evidence we have that there is no flying spaghetti monster.
Our evidence that the flying spaghetti monster doesn't exist is exactly as good as our evidence that an omnipotent creator doesn't exist.