|The Kojin beast tribes directly go against this idea. One of the main characters in those beast tribe quests is a minor kami. And everyone pretty much takes it at face value. Even when almost everyone forgets the kami in question since one of the other characters had the same thing happen to him when he was much younger. So... something is certainly going on and people call whatever that something is kami.
In addition... the Twelve as a religious concept is very, very, very old. The Allagans were worshiping the Twelve before they discovered aetherochemistry and started on the route that would lead to them becoming aethists as a nation. In fact... in Lore Book 1 it says that religion pre-dated magic and magic started out as people praying to the gods in the 2nd Umbral Era. Magic was just when the prayers started doing something extra. The 2nd Astra Era afterwards was marked by churches and religion being the de facto government because they had all the mages (and the fire power that came with that). It wouldn't be until the 3rd Astral Era that the Allagans would decouple religion and magic from each other.
If you were to ask me who the Twelve probably were... I'd say they were most likely the first set of Warriors of Light blessed by Hydaelyn, probably before the 1st Umbral Calamity ever happened (which is conveniently before known, recorded history starts). You look at all the stuff we are capable of doing and then apply a thousand years of re-telling of our story and making it seem even more epic then it really was and I wouldn't at all be surprised if people would think we were gods.
Now that view of the Twelve not directly supported anywhere in-game, but given that each culture has its own gods and they aren't universally shared, I don't think the Twelve would be based on anything so fundamental as how many shards there is. Besides, there were thirteen shards to start with, and no one knows when the 13th Shard was Flooded with Darkness compared to the Source's history. We also have a much better explanation for why there are twelve eorzean gods in-game and it's linked to another fundamental principle. Which is that there are six aether elements and that each element has two aspects, so... the twelve elemental aspects of aether each have a deity associated with them.