For example, if you're an evangelical Protestant and you have some thread where you want to discuss a topic specific to your religious tradition with others who hold the same belief (let's say a debate on the scriptural source for prohibiting alcohol), you wouldn't want a Catholic to disrupt the thread by coming and attacking the doctrine of sola scriptura. The reverse would also be true: say there's a Catholic thread to discuss the merits of John XXIII's papacy, you wouldn't want some evangelical protestant to disrupt the thread by arguing the papacy is illegitimate and so on.
The confusion on my part stems from the fact that the "caucus" system in reality doesn't seem to restrict based on those logical guidelines. Here we have a thread about someone's conversion to Evangelical Christianity that's really only appropriate for Evangelicals to comment on, but it's open for anyone to say whatever they want. The reverse example I cited was a thread asking freepers whether they heard a pro-illegal alien sermon on Sunday, and it's restricted to Evangelical/Reformed freepers only. Why? Are we to presume that mainline protestants, Orthodox, and Catholic Christians don't have any pro-illegal alien pastors giving sermons? Are we to presume that only evangelicals are concerned about their pastors promoting illegal immigration? To restrict a thread like that makes no logical sense.