"I do not take the position of ontological naturalism; instead I take the position of methodological naturalism. I define ontological naturalism as "nature is all there is, and all basic truths are truths of nature". I define methodological naturalism as "the best way to understand and seek knowledge is to reference natural causes and events." I differentiate between the two by stating that methodological naturalism says nothing about the supernatural other than that it is not the best way to seek knowledge."
But here's the thing. How can you presume to the second without assuming the first to be true? Otherwise you have committed yourself to saying that you don't know about how the world is, really, ontologically (what exists) BUT you are going to pretend that "the 'best' (are there other ways?) way to understand and seek knowledge (presumably of what you don't know exists) is to reference natural causes and events." And what does that mean, exactly? Is it the same thing as reason and evidence? But what if that reason and evidence points to something "supernatural"? You are still unclear about your fundamental commitments in terms of both ontology and epistemology. How can an epistemological program of methodological naturalism lead to anything "outside" of nature? And if you don't commit to ontological naturalism, then why a commitment to epistemological naturalism?