Here's my take on it, I accept that on some points I'm probably wrong about things, but this is the way I see Gaider's statement on the non-existence of atheism in Thedas.
Religion, and faith in general, is the human reaction to the mystery of the universe. The good ol' question of 'why?'. Each faith tends to think it has the answer, or at least are closer to it than anybody else. A lot of people call themselves atheists, but are in fact closer to agnostics or even believers than they realize. A true atheist belives that there is no supernatural of any kind whatsoever. That the natural world is all that exists, and that it came to be by happenstance or accident of nature. And that all there is to it. No God, no supreme beings that had a purpose behind the creation of the world, no Star Warsy Force that binds the galaxy together and runs through all thing things. There's the natural world, and then there is fantasy and superstition. Most people I have talked to, even if they call thmeselves atheists, and do not believe in God, will accept that there may be something completely outside of their own experiences that is driving this universe, or at least led to it coming into being.
In Thedas, faith in a higher power is pretty easy to have. It's also pretty dang easy to be completely baffled or frustrated by the mystery, and deciding to stop trying to figure it out. What is not easy, what is almost impossible to do in a fantasy world like Thedas, is believe that the natural world is all that exists. A short trip to the Circle will cure a person of that kind of delusion.
Fact is that atheism, as we here on Earth see it, doesn't exist in Thedas. The devs(and I beleive Gaider in particular) have said this before. This is because Atheists have a pretty easy time here on Earth. It's pretty dang easy to deny the existence of a higher power when you're not confronted with the existence of the Fade, spirits and demons on a semi-daily basis. When a person next town over or the guy just down the street, or even your own freinds and neighbors are mages, or are confronted by the powers beyond the Viel, belief that the natural world can't answer everything is pretty much second nature in Thedas.
This is because the natural world, which is all a true atheist believes exists, doesn't exist in Thedas. Therefore atheism, as we know it, exists as much as Christianity does.
Even if they belive wholeheartedly in Christ, a player can't just insert Jesus into the world of Thedas and say that their character is a Christian. They can certainly allow their philosophy about life, doubtlessly shaped by their faith, to guide their character's own outlook. But there are limits to that.
So while a player can certainly make a character who thinks everything the chantry says is a load of bull, and thinks that people who believe in a higher power like the Maker are deluded, what they cannot do(without being deluded themselves) is think that the natural world is all that exists, as there is no natural world. They can believe that all there is is the world of Thedas and the Fade, that spirits are not divine, or have any inherant power over the people of Thedas. But you can't deny their existance. Their divinity, yes. Their existence, no.
I admit that my definition of Atheism may not fit yours, and that you may quibble with what atheism means or doesn't mean. And that may be all this thread is about, a simple miscommunication about the definition of words. But this is the bast way I can explain what I think Mr. Gaider meant by his tweet.