Mike,
Let's clarify something here. Scientific methodology makes no statements about God's existence because there's no way to conclude scientifically about something that can't be defined. "Supernatural" entities aren't excluded from MN just because they share some attribute of supernatural-ness, but because
there's no reason to assume they're even there at all.
Methodological Naturalism could in fact conclude that there's a God if there were any objective evidence of His existence. The absence of such evidence leads most of us to assume that God is either nonexistent or just irrelevant to scientific inquiry, but believers are adamant that this pretend (excuse me, supernatural) entity must be considered as part of empirical evidential inquiry. However, the terms empirical and evidential pretty much mean that science ignores any claim that can't be supported with empirical evidence. If scientific methodology were to introduce invisible, undetectable entities, where would the list end?
This is why creationism at its basis is anti-scientific. If I have to
assume the existence of a creator, and
assume that there is an objective way to verify this creator's existence, and
assume that belief in this creator expands our understanding of natural phenomena, and
assume that everything is the way it is because that's the way the creator wanted, and
assume that scientific data which don't support any objective notion of purposeful design should be ignored, and
assume that natural law can be nullified at any time through the intervention of the creator, and
assume that nothing in Nature is the product of mindless processes even if it appears to be, then I might as well give up any hope of meaningful scientific endeavor.
regards,
Esteban Hambre