The Solution is Just a Myth
Worldbuilders are often faced with a familiar problem: they’ve created a fantastic world history of how the fictional gods of their world stole the ability to use magic from the primal forces of the universe and gifted them to humans. Only they later decided that maybe they don’t want gods to exist in their world. And that whole ‘primal forces’ thing, maybe axe that too. And so they’re left with a great and compelling story of how humans learned magic that no longer works in the context of the fictional world. So what to do? One solution to this problem and the many just like it is to keep that story, but instead of having it be confirmed, have it exist as a myth, legend, or piece of folklore. How exactly humans learned magic, maybe no one knows, but the story remains.
This same solution also works for fictional elements that seem to contradict or be at odds with one another. Myths often don’t make sense and that’s okay. They’re myths. So if worldbuilders want to include competing histories of how their world began, or competing theories of how it works, it is easy to do so in this way.