In the context of your hypothetical, you are presuming exhaustion of all possible physical explanations (you suggest, after all, that the supernatural explanation was not the assumption you started with). Indeed, to reach your conclusion that the supernatural explanation is a fact, it is a necessary prerequisite that you exhaust all scientifically plausible, physical explanations.
And (staying with your hypo), since science is the vehicle by which the exhausted physical explanations were necessarily explored and discarded, science would also be the vehicle by which the ultimate supernatural explanation was reached. So certainly -- science would be "capable of recognizing" (and indeed be the vehicle for recognizing) this supernatural explanation.
This, of course, renders your parenthetical meaningless. The starting assumption must be that there exists a physical explanation. If the starting assumption is the supernatural, you will never rule out or even examine the physical, and consequently your supernatural explanation will be inherently implausible.
Now, are you suggesting that science, as of today, has examined and ruled out all possible physical explanations for either biological diversification and development or for the genesis of the first reproducing organisms?
You're still misunderstanding me. What I'm saying is that if I had been confronted with the situation I described, a supernatural explanation is not the assumption I'd start with. However, since I'm the one coming up with the hypothesis, I can posit any initial facts I like, and the initial fact I'm positing is that the cause of the phenomenon I'm describing is indeed what would be termed supernatural. It's not a "conclusion" I've reached; it's merely the initial conditions set out in the scenario.
So given those initial conditions (which the scientists conducting the investigation wouldn't be aware of at the beginning), would the scientists be capable of figuring it out? That is, would they be able to determine that it wasn't, or in all likelihood wasn't, the result of a non-"supernatural" cause?
Sorry, I should have addressed this in the same post.
To answer your question, no, I'm not taking a position on that. What I'm arguing against is the notion that such an exercise is inherently unscientific.