While looking up the subject of Plantinga's Evolutionary Argument Against Naturalism (EAAN) I found this exchange of posts in 2012 between John Wilkins and Plantinga himself. But my interest was mainly in this form of Plantinga's argument:
The argument has at least two forms, one with a stronger conclusion and one with a weaker. [...] The weaker argument has the conclusion that one who accepts N&E has a defeater for any philosophical or metaphysical beliefs he has—beliefs such as that Plato was right (or wrong) about the forms, or that there is (or isn’t) such a thing as objective right and wrong, or that there is no such person as God, or (Darwin’s example) that “the Universe is not the result of chance”—or naturalism itself. These beliefs are of such a sort that it doesn’t seem to matter, for fitness, for survival and reproduction, whether you hold the belief.
For reasons which will become obvious, I won't discuss the validity of the argument. Instead, let's see where the possible conclusions take us:
Naturalists may or may not accept the validity of the argument, but an informed naturalist will observe, from the results of psychological research and observation of the history and current practice of philosophy, that the conclusion of the argument—that we cannot trust our cognitive faculties when engaging in metaphysical or philosophical reasoning—is inescapably true.
Plantinga, on the other hand, doesn't care about the validity of the argument since he rejects a premise, rendering the conclusion unsound. Does that license him to engage in metaphysical reasoning? Of course not; the evidence that the conclusion is true doesn't go away just because you rejected the argument. So the evidence says that Plantinga is just as likely to be wrong about his metaphysical or philosophical arguments as the naturalist is, including about the EAAN (which for all its use of mathematical notation makes little attempt to engage with evidence).
So we're left, as Wilkins suggests, with skepticism about metaphysical arguments—which seems to be pretty much the right place to be. We can and should distrust any attempt to do reasoning in the absence of independent error checking; scientists handle this by testing theories against reality, while mathematicians formalize as much as possible and employ automated proof-checkers and similar tools. Of course this leaves philosophers out in the cold, and the idea that scientific investigation of cognitive reliability can undercut philosophy will doubtless lead to cries of "scientism!", but that's just the way it is. Philosophers can always learn to pay more attention to science...
That leaves two open issues. One is this: given that we are skeptical about metaphysical reasoning, does that mean that we should require agnosticism about existence claims, or should we reject existence claims not supported by evidence? It is clearly foolish to assume that all such claims should be treated as 50-50 probabilities (though that doesn't stop Plantinga from trying, in the interview reference in the previous post). Taking a minimalist view of what exists is more likely to produce reliable results.
The other issue is: what of Plantinga's claims that non-naturalism would explain reliable cognitive faculties, when the actual evidence suggests unreliability? Plantinga's position may not be self-inconsistent (whether or not EAAN is a valid argument), but it is inconsistent with evidence.