FOLLOW-UP: My note in the edit was due to a mistake in the implementation, kindly pointed out by OP via email. It is now fixed, and this thread appears in roughly the same place on both sites (there is some lag between the RSS feed that I use as my source and HN proper, so I wouldn't expect an exact match even if I did no re-ranking at all). It is, however, easy and interesting to spot which articles have been penalized; there's an NSA article at the bottom of the front page right now that's at the top of my penalty-free page.

I'll be modifying my page to highlight penalized items and calculate their penalty when I have a bit of time.