Agreed. The distinction I'd make from here is that those foundational epistemological axioms don't necessarily require an *explicit* metaphysics, even if they require an implicit one.
The physicist takes as axiomatic, explicitly or implicitly, that reality is consistent, that it is knowable (at least in part), and that physical matter is a relevant object of study. Those axioms are, it would seem, sufficient for the scientific method.
Under those axioms, metaphysical truths remain in a numinous realm beyond our ability to study. One might admit those metaphysical presuppositions are necessary for doing physical science while not admitting them as relevant objects of study.
Thus, like any logical system, science needs axioms to get going, but that is an implicit metaphysics; science may remain agnostic about other metaphysical pursuits.