It's not really clear whether those categories are mutually exclusive.
Anyways, Deep-folk got enough right to make a pretty big impact. They weren't flat-earth Atheists, they just viewed the Aedra and Daedra as pervertible forces of nature rather than infallible gods ever beyond the ken and yoke of mortal effort.
This, and that even the natural laws of Mundus can bend when applied with enough force and rejection.
But it should really be stressed that they're not flat earth atheists. They knew the gods existed and no, they didn't worship reason and logic (that'd Julianos worship for ya), but they wished to transend far beyond the gods, to become one themselves and go back to the first stroke of Anu and Padomay, something not even the most altmer ever consider. They were extremely high level metaphysicists, who knew how to create their own loopholes, divide by zero, and had a thing for music.
Their short comings were that they did not know love, and the absorbicide to become the Numidium was a bit of a rush job.