I think the idea is that when you flag or downvote you have to provide a comment on the action, and that comment is then displayed when someone asks for a list of downvotes and/or flags. Those comments are not part of the regular comment system, and one can't reply to them.
It's what happens on Lobsters, but whether or not it makes a difference is hard to say. The traffic is small enough that I doubt the effect is properly measurable.
Right, but however you expose that information, aren't you just providing nucleation sites for meta-debates? This is a site that practically begs users to generate opinions about everything; you can't even pick the background color for your blog post without potentially sparking a 10-comment subthread about it. Off-topic meta arguments are arguably the biggest problem comment threads on HN have.
It's what happens on Lobsters, but whether or not it makes a difference is hard to say. The traffic is small enough that I doubt the effect is properly measurable.