>>42266467 (OP)Well, lets say that ponies are atheists, hypothetically.
They live two goddesses who control the sky. One of them is directly obeyed for over 1000 years and beloved. The other, though reviled, may shape their dreaming worlds if she wishes, and so change who they are without anyone knowing what she has done. Luna, in this way, represents a power equivalent to the possession of demons and angels.
If ponies are athiests, despite the princesses looking like gods and acting as gods, and despite the ponies acknowledging their greatness and forming their society around them, this would imply something. If the ponies are athiests despite being exactly like thiests, then this would mean that the ponies are athiests specifically because the princesses are real. That's the remaining difference. The princesses are real, and people, and are a specific way which cannot be projected onto freely and subjectively. This would imply that there cannot be a religion focused around a real god, and that worship of a true god in the flesh, just a person god, would be considered atheism. Theism would imply falsehood.
If the ponies are thiests, this wouldn't mean anything nearly so interesting.