You're ignoring the 'think it's important that the point is raised' factor. If there was a user-visible flagging mechanism, then a hate-to-be-that-guy would use it and never feel any urge to make an annoying post, win-win. I strongly doubt that most people claiming to 'hate to be that guy' are lying.
I do realize that, which is why I said 'user-visible'. Flagging as HN currently has it can be used for moderation purposes, and for downvotes in extreme situations. But a user-visible flag would provide a warning to users that an article is fluff or otherwise problematic, and possibly attract more discriminating attention.