BINGO. As far as the distinction between the two, I think it is generally pointless. Even if there were a creator, I would avoid lumping everything into one category or another. I would prefer extradimensional explanations for deities and demons, for example - in general, render the world we can see as a subset of something more. Regardless, natural/supernatural is not the best way to look at these questions.
As I see it, though... the existence of a creator doesn't have to be an
a priori assumption. Granted, it may be so in the majority of cases, and certainly most people don't reason their way to that decision. We are often conditioned to believe or disbelieve; we either retain our conditioning, rebel/convert, or just lose/gain interest for a variety of emotional or social reasons.
As concerns methodological naturalism, I see it as a pragmatic device that does not claim to serve the determination of complete and absolute truth. It is useful and continues to prove its usefulness. The question remains, is there an actual methodology which incorporates the presupposition of a creator (or at least a "supernatural" world)? If so, what does this methodology look like and what are its verifiable results?