Meracydia/Miqo'te/Azys La speculations (spoilers)

[finiteHP]

I can't jump right to they worshipped the Twelve, but the symbols that we use for the Twelve gods did exist in their era according to the Version 1.0 Allagan Runestones, which displayed said symbols. The weird thing is ... why would they have a symbol of Menphina and treat it as a Goddess? I've said this before - they probably don't believe in a goddess of the TWIN moons considering one of the moons in that symbol is one of their military projects. Then again, back when that symbol was created, the lesser moon wasn't an Allagan creation. I have no idea how they're going to deal with that on the dev. side.

Two explanations come to my mind. One I think is plausible, the other is darksteel foil hat territory.

The plausible one is a case of appropriation. The Allag had these symbols in their temples. Some or all of them were representative of their deities, while others could have been religious in nature but not of a distinct deity. An example in real life of the former is the theory that the Christian halo was taken from the Egyptian sun disc (especially the early representations of the halo that are a filled circle of light). I can't think of an example of the latter off the top of my head so I'll make up an example. Imagine someone looking at a mural of angels and deciding that those are individual gods in a pantheon. This explanation even works for the Allagans worshipping the Twelve. At the time they used a different symbol to represent at the very least Menphina. Sometime after knowledge of Dalamud was lost someone important decided "you know, this symbol in this ruined temple looks just like the two moons. It must be what they used to represent Menphina and her loyal hound. Let's use it as a way of getting back to the root of the worship."

The foil hat theory is that this is the Allagan symbol for Menphina. There were two moons and when they launched Dalamud they decided the lesser moon's orbit would be a perfect place to put it so they somehow got rid of Menphina's loyal hound.