The "Boundary" Issue in the Skeptic Movement

As alluded to in my post about Bill Maher, a hot topic among skeptics right now is the proper bounds of skeptical inquiry. Massimo Pigliucci, contributor to Skeptical Inquirer and blogger, has some thoughts on the matter here. He ponders why if the domains of the skeptical inquiry, political philosophy, and atheism are are so well defined, do we so often see so much "crosstalk" between them:

Because the three areas in question do have a common underpinning, as illustrated by the diagram accompanying this article: atheism, skeptical inquiry, and political philosophy are all exercises in critical thinking and rational analysis. The differences among them is in the relative role that philosophical and scientific/empirical considerations play in each case.

That is why, for instance, I can coherently say that Penn and Teller are wrong about their libertarianism and about their position on global warming: in the first case, I am talking about philosophy, in the second about science. There is, of course, much more leeway in the first than in the second case. That’s also why there is no contradiction in me praising Bill Maher for his political views and yet thinking of him as a hopelessly inept commentator when it comes to his opinions on medicine. To consider one more example, this is also how I can agree with Dawkins’ and Coyne’s philosophical positions (and disagree with “accommodationists” like Ken Miller) and yet distance myself from them on the ground that I think they are stretching the tools of science beyond what is reasonable.

In Massimo's view, the problem is that some people talk about scientific issues using the discourse of their political philosophy or religion, talk of religious issues in scientific terms, and so on. I don't think he's saying that these areas are "non-overlapping magisteria," rather I believe he is saying that what counts as sound reasoning in one discourse doesn't necessarily work in another. Thoughts?