I’m an atheist so I’m inclined to side with your sources, alas I cannot.

The three websites listed were The Guardin, The Independent, and the website of the university who comissioned the study (wasn’t the actual study page). I did everyone a favor and looked through them. The University of Rochester & UC looked to be similar but you (and the articles) interpreted one as being mean and the other as being less charitable. The Rochester one has week terms and small amounts of data, the UC one hasn’t yet been peer reviewed.

The last one, which seemed to be the most rigorous, does not seem to be conclusive to me. Like, if I told you right now white people are smarter than blacks on average I’d be right. Obviously though, it doesn’t mean race has anything to do with it. If we looked into the actual factors it’d probably be almost exclusively their socioeconomic background. In the same token, this looked for one variable and then concluded that test results are essentially because of that variable. What you can do is refute the claim religious kids are always smarter. What you cannot do is then conclude atheist children are smarter, because it’s carrying an implication that simply for the fact they’re atheist they’re more likely to be smart without looking into other variables.