If there's one critique that I believe is paramount it's that HN has, due to its readership, an ethical obligation that goes beyond making discussions all nice and civil.
Political issues are obviously divisive and it's perfectly fine to keep stuff like the El Paso massacre of the front page. But when hot-button issues intersect with technology, the HN readership is in a position of power, and shouldn't routinely be spared the anguish of being reminded of their responsibility.
Yes, articles about, for example, discriminatory ML do often make it to the front page. But in my impression, that topic (as well as employment discrimination, culture-wars-adjacent scandals in tech academia etc) are far more likely to be quickly flagged into oblivion than similarly political takes that just happen to be in line with HN's prevailing attitude (e.g. cloudflare-shouldnt-ban-<x>).
The article impressively articulates what toll divisiveness takes on the moderators: Even if I read the same ugly comments, I am unlikely to experience the sharpness of emotion that apparently comes with considering the community one's baby, and making it's failures one's own. When such divisiveness is then reflected in the "real world" of mass media, the pressure only increases.
But as this article shows, abdicating the responsibility by keeping the topics sterile is similarly suspect, in the sense of fiddling while Rome burns. I believe a willingness to confront the ugly sides of technology with some courage of conviction would eventually be recognised, even if it may occasionally involve a bit of a mess.
Funny, I thought HN's prevailing attitude in the case of the recent ban of 8chan was, hell yeah, good riddance to those reprehensible twats. (Which, personally, annoyed me, because I believe that even the deplored should have a space for communication.)
So I doubt if reading the top comments is a very objective method for evaluating controversial discussion (it has a strong correlation, but maybe not the best). Often, I see very heated discussion and competing comments moving up and down until nobody is interested in spending more energy in the debate.
P.S: Invasive profiling and tracking can be a very effective (and possibly, the only) method to uncover insights on the dynamics of online forums like Hacker News. If we track users' every move, it could make great contribution to sociology and psychology researches, and may even help answering unsolved questions in order to building a better community for everyone. Unfortunately, it's too dangerous and unethical to use, I won't support it, but I'm always curious to know the results.