One of the comments mentions this: "Alright, doing some investigating it seems that they are saving the Pqs preferences based off of the instance ID of the pqs object, which, according to unity's own documentation, changes between runs of the game, hence why its saving 10 trillion different copies of the same data" So, somebody didn't notice a "changes every game" instance ID was in the path and/or data. They thought…
Coming from a Linux background, what is the windows registry and why do things need to write to it? All I ever read about it seem to be horror stories. Can't you store stuff alongside the install? Or in some user data location?
It's a centralized, high-performance small key value store that's the alternative to writing a million config files in random places.
It's arguably much better in my experience. E.g. one of the never-ending headaches I always have on Linux is updating config files when a package updates. There's no automatic file merge in general (hence .pacnew and such) so you gotta do it by hand (and not everything is available with the foo.d/ hack). The registry already operates at the value granularity so it bypasses this kind of issue.
And as a developer you don't have to worry about some things you might not think about, like the trade-off between corrupting your config files with in-place updates vs. having to create a new file and replace the old one after every config change.