I personally think that we're not gonna learn they're exactly as they appear so far, even if they're definitely not false gods. Alliance raids don't get as wild as normal raids, but they still go pretty crazy, and there's plenty of room for our expectations to be twisted and turned around. In fact, I expect it, because there's clearly framework for additional story than just 'the Twelve are real and we're throwing down'; if they don't have anything else going on then the two new characters they introduced are gonna have very little to do.
My main evidence there is that even the four gods we've already met have had symbols or tools that could only come from man; Byregot has a blacksmith's hammer, Azeyma has paper fans, Nald'thal have measurement scales and their symbol is outright mentioned to be a shell that's an ancient form of currency. This kinda knocks out a lot of the cleanest origins; they can't be of Ancient origin (since they wouldn't know a blacksmith if Gerolt smacked 'em in the face), they can't be of alien origin (since the cowry comes from ubiquitous shellfish), and they can't be of some kind of primordial origin (since a paper fan needs a creator). At least, not without some changing of shape and concept over time; even if Eorzean religion is 'objectively correct', it seems more likely that rather than them getting it right, that the deities changed form to fit the religion, at least to some degree.