Not entirely sure, I've wondered a bit myself.

The main one I come back to is that if a comment is worth both -4 net points and nigh-invisibility with the text fading, it's probably worth more. And only people with > X points (200? I think?) are capable of down-voting on -4 comments. Collectively, they serve to be stronger punishment for truly bad comments, controlled by people who have been here longer / contributed more, who probably know this behavior and vote accordingly.