A defeasible presumption in favor of proposition p is not evidence for p. In a legal proceeding there is a defeasible presumption of innocence (POI): one is presumed innocent until proven guilty. For example, Jones, who has been charged with Smith's murder, is presumed to be not guilty until such time as the presumption is defeated. But this presumption is not evidence of Jones' innocence. It is a rule that governs the adducing and evaluating of evidence. The attorney for the accused does not attempt to prove or provide evidence for Jones' innocence; his task is merely to rebut the positive arguments of the prosecutor. Thus POI does not play an evidential role but a procedural role: it amounts to a placing of ther onus probandi on the prosecutor.
In Why the Burden of Proof is on the Atheist, Ralph McInerny seems not to be clear about this ; he seems to confuse an argument for theism with an argument for a presumption in favor of theism. He writes,
I am asking whether the skeptic is justified in calling into question the truth of 'God exists.' Why not put the burden on him? Why not insist that he is attempting to convict of irrationality generations of human beings, rational animals like himself, whole cultures for whom belief in the divine and worship are part of what it is to be a human being? Were all those millions, that silent majority, wrong? Surely to think something against the grain of the whole tradition of human experience is not to be done lightly. It is, need one say it, presumptuous to pit against that past one's own version of the modern mind. This suggests that the present generation is in agreement on things incompatible with belief in God. Or that all informed people now alive, etc. etc. Meaning, I suppose, that all present day skeptics are skeptics.
Is there thus a prima facie argument against atheism drawn from tradition, the common consent of mankind both in the past and in the present time? I think so.
In this passage McInerny appears to be confusing the question whether there is a presumption in favor of theism (so that the onus probandi rests on the atheist) because of common consent with the question whether common consent amounts to an argument for theism. That God exists is a substantive claim made within the dialectical situation in which theist and atheist confront each other; that the burden of proof rests on the one who denies it is a procedural claim that helps define the dialectical situation.
McInerny begins by speaking of shifting the burden of proof onto the skeptic but ends by speaking of an argument against atheism. It may be that common consent is a good reason for presuming theism to be true until shown to be false without being a good reason for the truth of theism.