You simply understand enough to know that there is always a better explanation, and you are not so arrogant as to assume you know what that explanation is.
Except that definitively deciding there is no god is making the same logical fallacy and equally arrogant. This is why I'm agnostic. Even if I personally feel there is no god, I can't say that with 100% certainty because I'm only human and there are limits to the human brain.
And it doesn't matter whats "proved" or not. There is a nice little saying that gives religious folks a loophole for everything: "God works in mysterious ways." You can rationalize that forever.
And it would actually lend support to the intelligent design crowd if scientist were to conclude the universe is a giant simulation.