I'm an atheist and I accept metaphysics.

Science is a methodological naturalism, not philosophy.

What does this even mean? The scientific method can lead to, among numerous other things, philosophical naturalism), since the scientific method is naturalistic. Note Popper:

A naturalistic methodology (sometimes called an "inductive theory of science") has its value, no doubt.... I reject the naturalistic view: It is uncritical. Its upholders fail to notice that whenever they believe to have discovered a fact, they have only proposed a convention. Hence the convention is liable to turn into a dogma. This criticism of the naturalistic view applies not only to its criterion of meaning, but also to its idea of science, and consequently to its idea of empirical method.

This is a red herring, because the concept of "proving empiricism" is a nonsensical concept. Empiricism is used because it's the only method that's been reliably demonstrated to be able to be used to build predictive models of the universe.

I would agree, if it was widely held that empiricism yields models, not truth. This, unfortunately, is not the case.

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