I believe there is an anchoring effect -- if you are just in a discussion where someone helps you understand the RISC-V memory model, it feels wrong to go into another thread on the same site and unload a string of epithets on someone who feels differently than you do about how doctors should get paid.
Environments where all people tend to think exactly the same are typically extremist in some way, resulting from some kind of polarization process that eliminates people that don't express opinion at the extreme of spectrum. They are either removed forcibly or remove themselves when they get dissatisfied.
One way HN stays away from this polarization process is because of the discussion topics and the kind of person that typically enjoys these discussions. Staying away from mainstream politics, religion, etc. and focusing mainly on technological trivia means people of very different opinions can stay civilized discussing non-divisive topics.
Also it helps that extremist and uncivilized opinions tend to be quickly suppressed by the community thanks to vote-supported tradition. I have been reading HN from very close to start (even though I have created the account much further). I think the first users were much more VC/development oriented and as new users were coming they tend to observe and conform to the tradition.
(I red your piece. I think I figured it out. The users actually select themselves on HN though in a different way. The people who can't cope with diverse community can't find place for themselves, because there is no way to block diverse opinion, and in effect remove themselves from here and this is what allows HN to survive. The initial conditions were people who actually invited diverse opinion which allowed this equilibrium).
Short version: it's because this place is less divisive that it feels more divisive. HN is probably the least divisive community of its size and scope on the internet (if there are others, I'd like to know which they are), and precisely because of this, many people feel that it's among the most divisive. The solution to the paradox is that HN is the rare case of a large(ish) community that keeps itself in one piece instead of breaking into shards or silos. If that's true, then although we haven't yet realized it, the HN community is on the leading edge of the opportunity to learn to be different with one another, at least on the internet.