This is going to get into pedantic sophistry, and an area of philosophy that I only have a cursory knowledge of, but I've been told in the past that the difference between atheism and agnosticism is semantics. That an atheist doesn't have a "belief" there is no God. They just reject the idea that there's evidence for or against God/gods or the supernatural, which basically corresponds with the idea of agnosticism, that there's no empirical experience to prove or disprove the existence of religious deities.
Picard saying it's possible there's "a greater reality than the one we understand" makes sense since the Enterprise runs into one almost every other week. But those realities are based in scientific/empirical evidence that the ship's sensors can usually make sense of. Even Q is looked at as some advanced form of alien performing acts on a level they can't understand, but neither Picard or anyone else thinks that it goes beyond something that will not be understood some day by science.
