There is no atheism in Thedas and I am a hardcore atheist in real life.
Atheism is not merely a lack of belief in deities but it is also a commitment to an objective reality. This means that in the real world, you not only have to not believe in any deities but you have to provide evidence for why.
Examples include demonstrating capability to logically denounce gods' non-existence, understanding evolution by natural selection, historical proof that religion and gods are man-made and is a failed science of sorts as well as other scientific theories such as Big Bang and Heliocentrism.
You can't just say "I don't believe in Zeus or Indra or Thor or Amun-Ra or Helios or Aphrodite or Kamadeva ", you have to give a reason why such as "Well scientifically, this is how lightning works, this is how the sun rises, this is a biological explanation for having sexual attraction and so on". You have to be able to explain why things like karma and reincarnation is ridiculous nonsense and how entities such as a large tree or a rock or a mountain have no divine powers.
The thing is in Thedas you cannot do this. Science in Thedas has not or probably will not progress to the levels needed to offer a scientific explanation of reality as opposed to a theological and/or metaphysical explanation of reality.
Additionally, while the Maker may or may not exist, people of Thedas worship other entities such as Fade Spirits and High Dragons as well. The ancient Elves worshiped the most powerful Elves as gods.
Having said that, one can certainly take a viewpoint of being indifferent towards deities. That is the viewpoint most of my characters in fantasy games take and have :- "I don't give a single f**k about you being a deity or not. You leave me alone and I leave you alone. If you meddle with me, I mess you and/or your followers as well as your shrine up."
You're confused. The fact that what we consider IRL to be supernatural exists in Thedas doesn't somehow make the world inconsistent with a mechanical theory of reality. When we talk about objective reality what we mean is that we can - as a matter of epistemology - define the reasons for things in terms of their mechanical properties (and by that I mean the mechanics by which they operate).
The study of magic is absolutely and purely scientific in Thedas. The fact that their rules of nature are different doesn't mean they're not scientific.