And yet if that was entirely the case, HN wouldn't be such an interesting place. This sounds very much like someone making fun of the attempts of rationalism/effective altruism "because humans are not rational but emotional beings". Yes, it is mostly true but not entirely true and that's what makes a difference.

I am certainly guilty of downvoting (not flag) people I disagree with but I also read the guidelines and will downvote or flag a comment that seems to originate from one of my ingroups that would violate those norms because I value this place.

And I have also been able to nuance my own opinions by reading a well-behaved (respecting HN norms) comment even though I don't like its vibe.

I didn't see the flag system being abused. The flagged comments I have seen were most egregious norm violations. Whereas posts are generally flagged when they inherently highly flammable. It's generally a edge case and some of those make it through with a little moderation warning as top comment.