Perhaps it is a semantic problem.
One possible way to look at supernatural is not an either or.
It can be include and transcend. As reason includes the purely physical and transcends it; the spiritual includes reason and transcends it.
There are things that can be known by science, but not all; there are things that can be known by reason, but not all..
Each as sphere including the previous, but more - transcending and including.
Perhaps to a degree, but mainly it's an ontological problem. It's the container problem: can a container be made of the same stuff it contains? If so, what contains the container?