Flags on HN are user submitted. they are just as emotional as reddit downvotes. If something reveals an uncomfortable truth it gets flagged.
HN is actually surprisingly good about this, so I disagree with your assertion.
Thus, you build reputation by acquiring karma.
It isn’t perfect, but the fact that folks with higher karma can “fix” the emotional flags of folks with lower karma, it helps.
Also, I’d recommend re-reading the guidelines: https://news.ycombinator.com/newsguidelines.html
Effectively discussions that don’t get upvotes do get penalized yes.