I'm with you that I like the idea of having a strong visual indicator to differentiate different posts, but studies in UE have proven that the age-old "use zebra coloring to differentiate rows" that was used in accounting notebooks and perforated printer paper in the mid-20th century up until the 80s draws users' eyes away from the content in order to differentiate. Basically it is annoying to our brains and slows us down, but programmers like straight lines and making things neat, so the aesthetic nature of the differentiation in color and its assumed practical purpose makes us erroneously choose it over the visually simpler option.
Interesting, I never read that, but now I'll have to see if I can find the study you talk about. Like I mentioned before I would rather increase the font size and then space things out a bit more, but that would offer less links on a page so it becomes a compromise.
Thinking of the type of audience HN attracts one would think people wouldn't have a problem bumping up the size in their browsers although that can be annoying to do.
A good UI should not introduce new colors or visual elements that are unnecessary. Zebra coloring of rows has its place, but not here. Don't need the lines between posts (lines are for grids, and this doesn't need one). Additional box around arrows unnecessary. Text too small. Contrast of white on black at top draws eyes too much to title and menu.
Basically, please leave things as they are or ditch this design. I know you've spent a lot of time on it, but you will not gain users at as high of a rate with the new design.