The clue to the answer lies in the reference you provided earlier…
In fact, science is not even equipped to answer the question of metaphysical naturalism. Since methodological naturalism focuses on naturalistic causes and effects to the exclusion of anything else, science cannot hope to find out whether or not anything non-natural exists without defying its methodology. A priori, the methodological naturalism of science precludes its operating in terms of ultimate metaphysics. When science then engages in this behavior on the basis of science itself, it is merely begging the question.
How then can metaphysical naturalism be held as true? Only metaphysicians, or philosophers (or even philosophers of science) are equipped to answer this question. But only in the case that one has good reasons to think God does not exist does one also have good reason to think metaphysical naturalism is true! Even then, the problems referenced in the footnote before must be adequately addressed. So, the methodological naturalist has no basis for embracing metaphysical naturalism. What is required for this basis is both good reasons to think God does not exist and a coherent answer to the critics. In any case, scientists do not have good reasons, a priori, to accept metaphysical naturalism. They are not even using the right tools for the question!
It is through philosophy that we can answer these ultimate questions. I would also add philosophy is not “second place”, but arguable the “first place”. The foundation of modern science is built on the branches of philosophy (logic, epistemology, metaphysics, ethics) and more specifically the philosophy of science.