I agree with your first statement, VR; but not with the second. If science's technique is premised on "methodological naturalism," then arguably, certain natural objects will be found to be outside its scope altogether. Little things like, e.g., life, consciousness, qualia, any kind of non-corporeal, all universals in principle, etc. Just because methodological materialism cannot access such objects does not necessarily mean that they are "not part of our world."