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"Good, you have studied about metaphysics. I'm happy for you. Do you now realize that it does not necessarily have anything to do with the supernatural?"

That depends upon which "scientist" you talk to, now doesn't it. LOL

Methodological Naturalism? ~ Alvin Plantinga

The above link is posted on my FR profile page, QUOTE: "...science is said to be religiously neutral, if only because science and religion are, by their very natures, epistemically distinct. However, the actual practice and content of science challenge this claim. In many areas, science is anything but religiously neutral; moreover, the standard arguments for methodological naturalism suffer from various grave shortcomings. .." Methodological Naturalism ~ Alvin Plantinga

MORE: ".. Since science is not a system of thought deduced from first principles (as are traditional metaphysical systems), and that it deals precisely with objective experience, science is not, nor is any theory of science, a true metaphysical system. ...

However, the claim is sometimes, and more plausibly, made that evolutionary theory, along with some other scientific theories, functions as a kind of attitudinal metaphysical system [Ruse 1989] Ruse, M: 1989. The Darwinian Paradigm: Essays on its History, Philosophy and Religious Implications, Routledge.

Ruse also describes what he calls "metaphysical Darwinism" [ Ruse 1992 ] Ruse, M: 1992. Darwinism. In E F Keller and E A Lloyd eds Keywords in Evolutionary Biology, Harvard University Press. (as opposed to "scientific Darwinism") which is indeed a metaphysical system akin to a worldview, and which has expressed itself in numerous extra-scientific philosophies, including Spencer's, Teilhard's, and Haeckel's, or even the quasi-mystical views of Julian Huxley. .. ~ John S. Wilkins (talkorigins)

1) Your quote from Platinga is evidence of nothing. It does not say in WHAT WAY science is allegedly religious. More importantly, it is not discussing METAPHYSICS. The claim you made is that metaphysics is about the supernatural; this is wrong.

2) "MORE: ".. Since science is not a system of thought deduced from first principles (as are traditional metaphysical systems), and that it deals precisely with objective experience, science is not, nor is any theory of science, a true metaphysical system. ...""

So? Darwin was talking about Locke's epistemology, not science. You DO know that epistemology is not science, right? You DO know why he mentioned Locke, don't you?
You have not shown in ANY way that Metaphysics is about the supernatural. Saying it is extra-scientific is NOT the same as being supernatural. Logic is also not scientific; it's an a priori system. That doesn't make it illegitimate.

I'll ask again, why did Darwin mention Locke?