The only way to study the universe 'scientifically' is by observation of and experimentation with the universe, underpinned by the body of knowledge obtained by the same means. Observation of the universe requires that things can actually be observed, tested and verified, and experimentation requires established principles based off such observations and past experiments. We can't tangibly experiment with or observe metaphysical notions, since they are abstract concepts with no material form. That isn't to say we can't speculate, articulate or explore metaphysical notions, just that such notions are not tangibly verifiable against physical reality.
''Quatzelcoatl created the universe, it is evident in that the universe is created''. This can't be tangibly verified because the argument is based off unproven abstract notions, that isn't to say the notion can't be explored.
Science derives from the natural philosophy of Socrates, and natural philosophy is just that; study of the natural.