RELATED: Deleting Comments After A Fix
Extended discussions are not what this network was created for. This is a Q&A Site. If you have a need for extended discussions, then either a set of question/answer edits is due (thus negating the usefulness of the comments that were indicative of the need for change) or the comment thread is off topic.
Off topic comment threads are garbage and clutter up the screen, and detract from everyone's getting to the root of the situation quickly. It's why we fold comments in the first place.
Having said that, the message is only triggered when it detects a repeated back and forth between two people in a short period of time. So if it's just two people going back and forth, that's either a thread-war, or it's just a conversation between two blokes. The chat rooms were created expressly for having just a general conversation. FWIW, We've been asking for some feature like this where we can tie a chat to a given Q/A for later lookup. Because sometimes things that get fleshed out in chat (where there's a more permisssive atmosphere) can create a good update to a Q/A.
Also, sometimes a person needs guidance on rewording their question instead of it getting locked and them getting frustrated. I know I've had that a few times where I and a post author have gone back and forth in the comments on how to get it right.
I also suspect (altho I've no proof) that it triggers a mod flag once that occurs so a mod can make sure that the discussion doesn't need to be cleaned up. As that is one of the responsibilities of the mod team (to clean up the garbage aka the things which just clutter the site) then I suspect this is also happening.
Long comment threads's are not good for the site. Chat is for fluid discussions. Use it.