I don’t think departing from an empirical standpoint helps us out of this conundrum, based on my stone example. Even conceptually, if we define the supernatural as whatever the universe prohibits, nothing supernatural can be said to exist in the universe without invoking a contradiction. Sure, that leaves it able to exist outside the universe, but then it becomes tricky to determine whether it could interact with the universe without invoking contradictions.
It should be noted that I’m not arguing that because the supernatural is impossible, God is impossible. I’m just exploring a problem I’ve had with the concept of the supernatural.
It sounds to me like we need to wrestle with the concept of "Law of Nature" first, here. If, as you said, the laws of nature are descriptive, even if substantively so from our understanding of them today, it seems that this fits in line with Methodological Naturalism, does it not?
Wouldn't fact be that if we're dealing with a God who is Autonomous from own own human wills and intellects, then we can specifically define the exacting parameters of what the notion of supernatural would entail, that in addition to the regular expectations of the natural we have in merely descriptive terms, we could have room to possible, although not necessarily, observe effects of supernatural events that are:
1) One time events that will not be repeated.
2) Imperceptible nudges within Nature that we'll not be able to gauge in "the moment."
3) Possible phenomena, such as Jesus supposedly worked, that are clearly out of the usual parameters for what we currently understand about the laws of nature.
My point is, the term Supernatural is ambiguous and without God telling us exactly what the parameters are for measuring such manifestations, we're at a loss as to what to look for ............ or when to look for it.
So, in essence, and if I do in fact understand you correctly, I think you're right about there not being any clearly decipherable mechanism or measurement by which to 'detect' God, unless He decides to enable a manifestation which we can individually, even if not corporately, deem as something distinctly "uber" from the norm. The point at which I stick here is with your implication that this will always result in a clear contradiction in all supernatural cases, 1, 2 and 3 that I've listed above.
For instance, let's say that the Big Bang was indeed ... done by God. How would we know? It's a one time event, and due to this fact as it pertains singularly to deep space and time, we can't discern that it came from God, although in the hypothetical instance I'm referring, He did it. And hence, we would not say that in that instance the supernatural event was a contradiction.