This is where the traditional definition of God diverges, to my understanding. He is viewed as exactly that, unbound. That does not mean that he does not work within the limits of nature, but he can go beyond them. In fact, even if he did not work within the limits of the natural order, would we even know it? Of course the better question is, would that then have an effect on us? (which has been your inquiry all along,
md0, that hasn't been lost on me) I suppose we wouldn't have any way of knowing.
The usual way God is viewed in the circles I frequent is as not physical, per se, but rather beyond the physical. I.e. metaphysical. I do not agree that the metaphysical has been proven to not exist [I should bracket this by saying I haven't really looks at any research into this as of yet, but it I would be interested in what methodology and evidence they use to arrive at their conclusions], which you started the conversation with. It is much like asking the other "big" questions like, does God himself exist. You can ask 10 different people and get 20 different answers, all with different reasoning. That's just the nature of exploring that which is [purported at the least to be] beyond that which we know. Of course, traditionally God is supposed to be knowable, but even that is bracketed by saying He is not fully knowable or understood.
I'm sure most of that was already known, but I said it anyway.
I guess my point is, how could you arrive at a sound answer for the existence or absence of the metaphysical? How would you observe that something is there? Or isn't there? What evidence would be useful? What would we even look for?
Personally, with all the other scientific breakthroughs and such and all the other things we have discovered, it would be premature to say that the physical is the end of the road. We've already tried saying that the earth was the center of the solar system, or that people got sick from curses, or that the atom was the smallest unit of the universe. We've broken through all those. Granted those are all of the physical realm, but I'd like to think my point remains.
Of course that says nothing to the question of God's existence, but I suppose everyone has to make up their own mind at some point.