Are skepticism and atheism non-overlapping magisteria?

Ever so often a fight breaks out among skeptics and/or atheists about how to deal with religious people. This time it was started by Jeff Wagg who is criticizing the skeptic conference Skepticon3 for being too atheistic. The organizer of the conference, JT Eberhard has responded (pretty well in my opinion) as has PZ Myers, who is a speaker on the conference.

Now, I make no bones about being both a skeptic and an atheist, so it is easy for me to just side with Eberhard on this, and dismiss Wagg out of hand. But would it be right? Looking at the comments to Wagg's original post, you'll notice some fairly prominent skeptics siding with him. It might be one thing to dismiss Wagg, a person who has flirted with anthropogenic global warming denial in the past, but I'll be damned if I am going to dismiss Eugenie Scott without serious consideration.

So, is atheism and skepticism non-overlapping magisteria, as Gould famously said about science and religion?

The short answer to that is NO. The longer answer is, on the other hand, more complex. Skepticism can be said to be a method, while atheism is a position related to a specific subject (the belief in the existence of deities). Skeptics are people who apply skepticism to all subjects, while atheists are simply people who don't hold a belief in a deity.

The group of atheists and skeptics are overlapping, but neither is by any means a subset of the other. Many, probably even most, skeptics are also atheists, but there are many skeptics who are still religious - some by not applying skepticism on that particular part of their lives, others by accepting that their faith flies in the face of evidence. Atheists, on the other hand, are often not skeptics.

Personally, I think that atheism is a natural result of skepticism (and it is interesting to note that the skeptics involved in this conversation are, to the best of my knowledge, all atheists).

So, what's my point? Well, what I am getting around to, is that Wagg might be right that a skeptic conference focused overly much on skepticism towards religion might be off-putting to some skeptics. But so what? There are global warming deniers showing up in all skeptic groups that I've come across - should we pretend that they are right? Or should we avoid the subject? Or course not. For skepticism to make sense, we have to apply it to everything.

This doesn't mean that we have to do it all the time, so if Wagg wants a skeptic conference that doesn't touch the subject of religion, that's great - he should go ahead and create it. Then the rest of us will choose whether we want to participate or not. If it is about ghost hunting, UFOs and cryptozoology, I'll personally give it a pass, but if it, on the other hand, is about woo and alternative "medicine", I'd be interested.

What Wagg shouldn't do, however, is to tell other people how to run their conferences, nor should he try to exclude subjects from being covered by skepticism. All subjects must be open to skeptical inquiry. Otherwise, how will we expand out knowledge and understanding of the world?