I think the reason for the two mechanisms for signaling is to differentiate between "this person is being a jerk/is misinformed", and "Nuke this comment from or

I think the reason for the two mechanisms for signaling is to differentiate between "this person is being a jerk/is misinformed", and "Nuke this comment from orbit with extreme prejudice". That way, the flag function's significance for spam/malevolence/badness doesn't get diluted by people who would be content to downvote.