Ultimately this question is not fundamental.
The fundamental difference is in world view.
On one hand a so called “scientific” world view is presented where mind itself is a product of material interactions.
On the other hand we have the theistic world view that all creation originates from and is sustained by a mind… i.e God.
In such a scenario, the dichotomy between natural and supernatural disappears into a dichotomy between what is accessible to scientific enquiry and what is not.
The fact is that only a part of reality/Gods domain is accessible to human beings… And an even smaller part of this domain is accessible to science. As it is, we have a blinkered view of God limited by our humanity when we do theology… Do we want to further blind ourselves by restricting ourselves to only what science can find out?
The more we think in terms of “nature” doing things… the more we have a tendency to view nature as having qualities that belong solely to God.