It was a reference to the featured article. It does not have any good or evil connotations. The author suggested that, like light and dark matter coexisting without any knowledge of the other's presence, the author coexists with conservatives with certain views (creationists). Stats show that they are out there in huge numbers, but he has no first hand account.

Here he is alluding to dark matter. So the light universe is our observable universe, the dark universe is the hypothetical universe made up of dark matter that we know has to exist, but so far have no means of observing or interacting with. That's the analogy he's making between the Red and Blue teams. They co-exist in the same space but manage to avoid interaction.

That was the meaning of that first bit from the article that OP quoted.