@ElysianFields Well, other people are at least suggesting it now too, so it's no longer just you (and at a site that has that problem even worse than Workplace.SE). Hopefully that means it's gaining traction.

For what it's worth, Interpersonal Skills.SE has suggested that the association bonus not be included for the purposes of the "Comment Everywhere" privilege, which would hopefully decrease the number of comments added to Hot Network Questions by excluding those that aren't already active on the site.

Thanks for the screenshots. It doesn't look so bad on yours, but it seems you have a much taller monitor than me (mine is widescreen 1280 x 800). I've added an additional screenshot to the question showing what I see. Perhaps the issue then is that we ought to decrease the size of the header and/or the whitespace above the first question to accommodate those with shorter monitors (which would include netbooks and tablets not on the mobile site).

I now see 3.25 questions instead of 2.5 questions. An improvement I guess, but I would prefer to see closer to 6 questions like on Stack Overflow.