The only issue I might have with it (depending on how it functions or updates), is due to the lack of a linear flow, it might be difficult to quickly find a story / link again without scanning every box.
I often come back to HN and read a link later, or check the comments later and so on. With a line by line link flow, I can quickly scan for anything I've clicked on or wanted to check out.
I'd suggest having the link colors change upon click through (right now they appear to just stay black). That would add a helpful visual cue.
Or even let me click and tag an icon on the story box, for future reference (equivalent to an "important" tag). Then I can scan the boxes faster.