That latter (more subtle) point is a possibility I suppose but even if it were the case it would likely reflect the unpleasant side of normal online psychology

That latter (more subtle) point is a possibility I suppose but even if it were the case it would likely reflect the unpleasant side of normal online psychology rather than anything particular to HN; and there is still a significant difference between cynicism/negativity and the bigotry and hostility claimed by the "harmful" comment and linked context. If all such reflex internet-negativity is being wrongly interpreted as representative bigotry by an external party that's still not a HN issue; and the moderation complaint is still very misjudged.