A few things are going on:
* Highly visible posts (on HN, you can get visibility early on by making top level posts. Very recent top level posts tend to be displayed at the top of the page) will receive more votes, up or down, than posts which are less visible.
* Votes are crude. I might see two comments which I think are good, and vote both of them up. But what if I thought one of those comments was not merely good, but excellent? I cannot communicate that to HN without either neglecting to upvote the merely good comment, or by 'strategically' downvoting the good comment.
Combine these and a good top level comment refuting a comment will likely receive more upvotes than a superb child comment refuting a comment, even if each individual reader in the thread would say that they preferred the child comment. Vote counts, despite appearing democratic from 1000', do not necessarily illustrate the will of the readers.
There is a third thing going on too:
* People love online drama and arguments.
Exhibit A would be Reddit's 'subreddit drama' subreddit, which does nothing but link to arguments on reddit for the amusement of the subscribers. Because of this, posts that are confrontational or take unnecessarily strong stances and indict large vaguely defined groups of people will rake in the upvotes. Maybe that is what HN readers want, but should that be what HN gives them? If the site ran itself as a pure democracy with no guidelines or moderator assisted shaping, it would all just be image macros and pictures of pets.
Top-level posts have a major visibility advantage over reply posts, and thus have a karma advantage.
I wonder if weighting a top-level post's score by the score of its children would help alleviate this. On one hand, there could be more rewards for trolling, since a troll that attracts popular refutations will be visible. On the other hand, a civil post that is both upvoted itself, and invites interesting upvoted discussion, will outrank the troll post.
A 100 point comment that is two or three screens down and buried in a nest of mediocre comments is almost certainly better than a 100 point top level comment at the top of a discussion. The later is a much more difficult and impressive feat.
Comments would have the same point values, but the value that is added to the user's karma score would be weighted. Getting lots of points would still make you feel good about your comment, but it would neutralize more ...strategic karma farming.
Oh, the irony.
If you want other examples of similarly egregious comments I'd be more than pleased to provide them, but we already have a perfectly functional example right here.
That it's not "top level" itself, well, I don't find it as much of a differentiator.
"Top level, or not" may not be something that you find to be an interesting consideration, but it is what I am complaining about. Since meta-conversation in general is not what I am complaining about, there is no irony.
It's a common pattern both here and on reddit (because top-level meta-commments really are effective for farming karma), and it should really be against the guidelines. Best case scenario: the complaint is 100% valid and on target, but because it is a top level comment and correct it will rise to the top of the discussion while the offending comments will be downvoted and buried at the bottom. Refutations for shitposts should be buried with the shitposts^, visible to those who decide to read the shitposts but out of the way for everyone else. We don't need all discussions "bookended" by shitposts and comments refuting shitposts.
^ Not buried by being downvoted of course (accurate refutations of shitposts should generally be upvoted), but rather buried by merely being the child comment of a downvoted post.