in the end it rests on the proposition we can confidently know all of reality and predict it down to the movement of an unseen atom
No it doesn't. We are allowed to simply say "I don't know." We don't have to have an answer, and we don't have to know that there is someone (deity of your choice) who does have all the answers. We're comfortable not having all the answers. Science itself is tentative.
That's agnosticism, not atheism.