There's little more useful to say here, other than I don't think most people would agree with your view of what HN is.
It's a discussion forum, not an exegetical seminar. "On topic" is whatever the topic of discussion is; and this is not constrained to the article.
[ ] My comment is on-topic and positive to neutral
[ ] My comment is critical
[ ] My comment is off-topic
You've got to select one. When viewing, the comment thread defaults to just showing on-topic, non-negative comments, but you can see the other stuff, too, if you want.
This solves two seemingly contradictory desires: the ability to read comments on things that interest you without having to fend off waves of negativity and wade through pools of offtopic text and the ability to speak freely.
Think of it as very roughly analoguous to the different sections of a newspaper.