What if you consider it as an optimization problem for the late commenter? You have to choose where to insert your comment, most likely there are multiple optio

What if you consider it as an optimization problem for the late commenter? You have to choose where to insert your comment, most likely there are multiple options. A root-level comment when there are already dozens is unlikely to be noticed; there is significant momentum behind the top comments, usually for good reason - whether jokes, clever insight, or a popular viewpoint. Instead, if you reply near the top in a context where it makes some sense, you skip the root-level graveyard and are almost guaranteed good placement with the downside of "overhead" due to the upwards chain always appearing first. Consider also that the penalty for being the 2nd, 3rd, or worse comment at root-level gradually increases due to the increasingly nested replies to each highly rated comment. If you assume root-level comments express opinions, minority opinions are also more likely to maintain good position in a reply comment such as the one you posited. Lastly, "trickle down karma" could be a factor. A quality reply to a root-level comment could enhance the parent comment's value and result in additional karma for them. Such situations could include biases like assuming comments which merited replies are interesting due to peer validation and thus reading them, and more fundamental added value such as uncited sources being given.