Chuck is in on it, he's fine. He knows and plays into it. But he's definitely not dumb. He can follow along with what Neil says just fine, even advanced topics that I can't follow as someone very interested in science. I know he can because he rephrases what Neil says in his own words and Neil would go "Exactly!" or something to that effect.
The comic relief act is just that, an act, for comic relief, and it's funny because it's working in a meta type way.