I see it like this, to be put simply. Gods are not gods in the traditional sense, rather, they are the artificial creation of
Engwith, a society of high minds and broad concerns. In their time, every people worshiped its own gods, which inevitably led to religious warfare. The Engwithans sought an end to it after a series of devastating conflicts. They devoted all their energy to finding the true Creators. Generation after generation, they analyzed the fabric of the world and unlocked its secrets, mastering the science of
animancy. One day they found an answer - except the answer was no answer at all. There were no gods to be found. Or if there ever were, they were gone. It was a terrible shock to them: If they could discover this on their own, how long until others would? How long before war and chaos reigned over a world without consequence? To prevent this scenario, they used their mastery of animancy to create their own gods to fill the void, utilizing a massive adra-powered machine at Sun in the Shadow to harness the souls of thousands of Engwithans assembled in the chamber - men and women, children and the elderly, all they could find - spawning the known pantheon. Each of them was crafted from an ideal, to give the kith not one, but many meanings to choose from in life. The surviving Engwithans then sent missionaries to the corners of the world to spread their faith.
The missionaries knew the secret, but never revealed it to anyone. They refrained from marrying, voluntarily extinguishing their bloodlines to minimize the risk of exposure. The entire project was almost ruined when Iovara ix Ensios learned the truth, by accident, due to careless missionaries discussing the subject openly at one of their temple.Her defiance and determination to expose the missionaries and their gods as fraudulent eventually coalesced into a popular movement that only grew bolder as the Inquisition formed and retaliated against Iovara and her followers - many of whom were former members of the missionary force. The size of the movement threatened to destroy the fledgling faith, until Thoas, one of the authors of the divine project, captured her at Ossionus, destroying her body at the Court of Penitents and imprisoning her in the adra cells below.
The belief in the gods Engwithans created spread throughout the world, eventually becoming the one true faith of the kith of the world, and their nature successfully obfuscated by Thaos and the Leaden Key.