There is generally no need to splatter crap all over the OS, but most do it because they're too ignorant to write a clean application.
Wot, you mean like yer typical Linux application which scatters files all over the place in locations
which are hard coded and cannot be changed if they don't suit your system? It's a long time since I've seen a Windows application which absolutely insists on putting stuff in "C
MyApp\Whatever" whether you like it or not, but this is routine for Linux stuff. It's not as if there's any consistency either, you can install half a dozen different Linux applications and they each have their
different idea as to where to put log files, and as these are all hard coded locations you can't decide for yourself to put them all in the same place.
And all these crappy little configuration files
are written in different languages so you have to learn each one, and if the worst comes to the worst (the GUI configuration editors don't do what you want) you're left with typing incomprehensible hieroglyphics into a text editor and hoping for the best? (OK so the registry editor can also get a bit painful, but at least you can't screw up structure and syntax in quite the same way that you can with a text editor and text file.)