And that is precisely the view that I am arguing introduces an unnecessary and unjustifiable conflict between (2) and (3). There’s no logical reason that one could not say “ground with the teeth,” for example, depending on what metaphysical aspect was being addressed.
The point that Dave Armstong aptly made is that Kelly is just begging the question for his Protestant view at this point. His “two views” make a number of assumptions that aren’t necessarily warranted from a Catholic perspective, and Kelly presents no argument for his own peculiar metaphysical view, nor even an argument that the distinction he makes was present in the authors he cites. In fact, by Kelly’s own admission, it is likely that Augustine did not recognize such a distinction, for if he had, he surely would have perceived the “contradiction.” From a philosophical perspective, Kelly, Schaff, and Pelikan are all begging the question.
From the metaphysical perspective, that’s not even a relevant distinction, because one could mean exactly the same thing even while saying something different. All Kelly is effectively doing is pointing out that they SAY different things, and then interpreting what they say according to his own metaphysical notion that these concepts are opposed to one another. His metaphysical justification is lacking.
Technically, “according to nature;” as applied in this case, then, according to the natural union in the person of Christ. “Real” and “physical” mean roughly the same thing.
Regarding Calvin’s belief, note two things. First of all, he says exactly (3): that by presence he means the real presence of a spiritual effect, not a substantial presence. From the quote you provided, “reality is here conjoined with the sign; or, in other words, that we do not less truly become participants in Christ’s body in respect of spiritual efficacy.” That is NOT presence in the sense of substantial or physical presence, which is what Augustine affirms, but rather is a mere conjunction of reality with the sign through an effect. From a metaphysical perspective, those two things are entirely different (which Kelly, Pelikan, and Schaff all fail to grasp because of their defective Protestant metaphysical commitments). Second, Calvin is arguing for a bare contradiction if Christ is not understood in Nestorian terms. He is saying that Christ is really present for participation, but not really present in His Body, which destroys the unity of the person (if Christ is a real personal unity, then where Christ is; He is in all His parts, just as where my body is, my soul also is as part of my personal unity). If you think otherwise, then it doesn’t prove anything except that you are misunderstanding what Calvin said as well.