Comments in the SE engine have always been ephemeral, temporary notes that should result in some useful change to the post they're attached to, at which point they become obsolete. We didn't want them, and didn't have them originally. We added them because people kept using answers to post follow up commentary.
A long stream of comments is a bit of a burden for future readers searching for answers to the question that was asked. You arrive to the page, see that the question matches your own and then find this seemingly fantastic answer that appears to address all of your concerns. But wait, there's a long line of comments under it - is there something perhaps sub optimal that you're not seeing? So you read them all, many times unnecessarily.
Whenever possible, try to make sure comments either present something of lasting value, that should be consumed with the answer but don't exactly fit within it or are removed when they are no longer relevant by flagging them.
That said, it's just an automatically generated message that accompanies a system initiated flag alerting moderators that there's a protracted discussion going on in comments. It's up to the moderator to decide what to do. Sometimes chat just isn't feasible for people in disparate time zones, sometimes answers just require quite a bit of explanation. As the moderators have been informed, the system trusts that whatever action they take (or don't take) is appropriate, and that's it.
Just please try to keep future readers in mind when comments get lengthy - comments that aren't essential reading to fully understand the answer (which can usually be moved into the answer) just create unnecessary reading - and that's what we're trying to avoid.