The thing is there is a lot to unpack there. A lot prescientific natural philosophy came from rich people (mainly men) that actual wrote stuff down and they were prone to thinking in terms of philosophy and the believe that the nature of reality could be derived from pure reasoning. People who might be in the position to know the relationship of caterpillars and butterflies were usually not in a position to write their observations down.
The notion of the scientific method, where stuff was not accepted without observational evidence and inductive reasoning from observation came much later. Social standing, and the connection of manual works with slavery probably plays a big role in this.
Then there is the nature of magic, in a reality where magic exists, then magic is as fundamental a force of nature as gravity or electromagnetism. However, we as players and game creators tend to model our fantasy worlds as if some or all of the magical world view of our ancestors was actually true.
Where you end up depends a lot on where you want to go and what assumption you want to make. Also, on the amount of rigor or not on the fundamental nature of magic. I am not sure we could really do a from the ground up take on magic because we have no idea on how it might really work.