I don't think anyone has been "secretly screwed". HN is a complex system consisting of different factors, including community, software, and moderation, that all have their proper place and do things the other parts can't do.* If there's a way to modify the
system to function better, I'm certainly interested, but I don't think mods doing their jobs properly is screwing anybody.
On the contrary, the things mods do—including downweighting top subthreads when they break the guidelines or aren't in the intended spirit of the site—are vital to why HN functions as well as it does (not that it functions particularly well; just that it could and would be worse). In fact, that process of downweighting top subthreads is probably the biggest thing we've ever figured out to improve thread quality, at least in recent years.
* Btw, if there were a way to have the community and software alone do what mods do, and thus eliminate the need for mods, that would be a day of great rejoicing on our part