My shot at interpretation of Nasuverse's cosmology
So I already made a post where I asked if physics are the true laws of the universe which some agreed to and others did not. Some did put it and explain it in a good way but I return to Case Files and F/GO and I'm left confused all over again. To explain my point, the franchise doesn't make it's mind over who created whom in Nasuverse, and why are humans the same in every mythology. Where is Adam and Eve in all this? Moreover, if science, the dominant system in the humanity's texture, is ultimately just a result of human belief, then how does research work? How does discovery work? Is what humanity achieved even real or whatever magical force retcons reality to make it appear so? I still have grippes with this franchise about its lore as though whatever writer can just easily decide it, like historical figures' gender, especially historical figures' gender (I swear historians there will choke their predecessor if they were aware of how much bullshit there is), but I'm more fascinated and too deep in the rabbit hole to escape this serie's worldbuilding.
So If this world has a loose lore, I'll just answer these questions myself:
Everything was created by the Abrahamic God, this also includes The Root (Akashik Records). God created the universe and it's celestial bodies with physics as the default system. These celestial bodies having varying levels of intelligence and will, as well as an access to The Root and planetary amount of cosmic fuel, that is mana, allowed them to defy the system and make their own rules based on Mystery, which lead to making their own creatures such gods, elementals, magical beasts, environments (Textures) and the culmination of it all, Ultimate Ones.
While they're doing that, God created Adam and Eve in paradise. And as the story goes, Adam disobey God and eats the fruit which ends up with both expelled to Earth as punishment. So all pure humans are descendants of Adam and Eve, and not a creation of the planet. if anything, Gaia copied the human template and used it for its own purposes.
To add more to the topic of humans, they are weird. They're part of nature but not forever. Little by little they're moving away from it, and with each discovery and new invention they weaken Gaia, stripping the mystery and letting the original laws reestablish themselves again. Which is inspiring to me at least. Humanity rediscovering the true laws of the universe (Truths) and using them to fight and triumph over what is the culmination of pulling the wool on the universe.
All in all: the Abrahamic God is the supreme creator, they created the root the universe and all that's in it. The Physics system is the baseline and original system. The celestial bodies are intelligent living organisms with direct access to the root and cosmic fuel that went wild with creating their own rules and creatures. gods, textures and other supernatural entities and phenomena are a distortion made by the rules put by the planet. Humanity are a creation of God and not the planet or it's gods. Humanity rediscovering the original laws weakens Gaia, and one day will fight and perhaps triumphs over her and the Ultimate Ones.