Atheists and theists often discuss the existence of God. Unfortunately, these discussions often degenerate into classic Christian apologetics where the main goal of the theist is to rationalize why his or her god doesn't conflict with rationality.
Before long they are rambling on about how to resolve the problem of evil or why god doesn't reveal herself. These problems only exist once you've accepted the premise that there is a god/spirit. This sort of apologetics has nothing to do with the fundamental question of whether god exists in the first place.
Now, Moran is usually pretty reasonable; but this argument is so thoroughly absurd and irrational that he should be ashamed to have put it forward. Let's abstract from the situation a bit to show why. Take a position, A, and a contrary position, B. Now suppose that A gives an objection to B. To this objection, B responds with an argument, whether good or bad, that the objection fails. To which A replies, "This sort of apologetics has nothing to do with the fundamental question of whether B is true in the first place." But this is demonstrably false, of course; B's argument was dealing with an objection put forward by A. What A is trying to do is irrational: he's trying to rig the argument so that his objections are never answered, independently of whether they can be, by dismissing any answer that might be made to them as 'apologetics that have nothing to do' with the original question.
So it is here. The reason theists talk about the problem of evil or the problem of hiddenness is that atheists typically raise these as objections to theism. To say that they have "nothing to do" with the original issue is to show that you have lost all interest in serious analysis of the argument and are merely trying to spin things your way. This is a fundamental problem with certain noisy atheists today: they argue like IDers of the least honest sort, because this is, in fact, a standard ploy of a certain kind of ID theorist -- to every response the evolutionist puts forward to an ID argument, they reply that this really has nothing to do with the fundamental question of whether evolution can really explain apparent design and, like Moran with theists, they take any sort of sophistication as a sign that evolutionists are merely trying to wriggle out of an obvious point. And this sort of response is wrong for general logical reasons, not merely domain-specific ones: to make it takes extraordinary, and baffling, ability to ignore the actual structure of the argument when it suits one. Reasonable people, on the other hand, will point out that arguments are bad rather than try to rig things so that their opponents can't respond to objections. It may well be the problem of evil is only a problem on theistic assumptions, if it is one; but that means precisely that reasonable assessment of the state of the argument requires looking to see whether it really is a problem on theistic assumptions or whether it only looks that way due to superficial analysis. If you are going to claim that someone faces a problem on their own assumptions, it's irrational to shout "Unfair!" when they try to show that, in fact, it is not a problem on their assumptions.
In any case, Moran has completely missed the point about the 'Courtier's Reply' that more reasonable atheists than he have liked about the story: namely, rather than taking it to show that arguments are irrelevant (which is frankly silly, and shows that Moran has not thought this matter through) they take it to show one way in which an argument can go bad -- namely, by a set of subtle red herrings. For that is, in fact, what the 'Courtier's Reply' is: a parable about fallacies of irrelevance used to muddle up considerations of relevance themselves. But it does not show that any particular argument is irrelevant, much less that any particular group of arguments is irrelevant, nor does it show that one's opponent is confusing what's relevant. That depends on (1) the quality of the grounds for thinking that the Emperor has no clothes in the first place; and (2) acceptance of those grounds by the opponent combined with a refusal to accept the consequences. You will recall that Myers, contrary to Moran's suggestion in the post, came up with the 'Courtier's Reply' to deal with people who accepted that the Emperor had no clothes, but denied that this was relevant. That is, the Courtier's Reply is given by someone who sees, or accepts that someone sees, the grounds on which the claim is made -- all the signs are there, the "dangling genitalia" as Myers puts it -- but claims that this merely shows that the person appealing to these grounds has no taste, and can't appreciate the finer points of imagination. And that is all: it's about weaseling out of a conclusion you already accept. The people it fits are atheists who accept that there is no God (although possibly also fideists who accept that there is no reason to think that God exists) but claim that to point this out is bad taste and shows a lack of sophistication. By transferring this without any modification to people who really believe that the Emperor is clothed -- who deny that the grounds for thinking the Emperor is unclothed are good grounds -- Moran has mangled the whole thing rather badly. The parable only works if the Emperor is, in fact, naked, and if everyone in the discussion sees that. You can see that this is, in fact, required for the argument if you actually read the thing. If nothing else, we lose the second requirement in the transition to theists.
It's unfortunate, too, because it makes Moran seem more unreasonable than he probably is. He ends by saying that he would be happy to discuss evidence for theism. This would sound somewhat more sincere if he hadn't just finished giving an argument for why he doesn't have to listen to any responses to any objections he might raise against this purported evidence. It could be that Moran just is not interested in the problem of evil or the problem of hiddenness -- that is, that either he doesn't actually regard those as fatal problems or that he doesn't think he is the one to be developing such objections. And then it would be reasonable to say that you really don't care what theists are saying in response to them. I suspect that this is what is really going on -- that he just doesn't have an interest in that particular kind of discussion. And that can be entirely reasonable. But it is also a personal thing, dependent on one's own particular circumstances; by trying to raise it into some general rational principle he is simply saying that atheists get to cherry-pick from the arguments on the table.
UPDATE: Larry Moran replied, denying the interpretation of the story. So you can see for yourself that he has mangled, and continues to mangle, the whole Courtier's Reply, you can continue reading here.