> (I haven't used a Mac in ages, but I assume the situation is very similar there, too).

It isn't. Well-behaved Mac programs use ~/Library/Application Support/ and ~/Library/Preferences/ for these sort of things.

GUI-based software that craps on my home folder doesn't last long on my system unless it must be there for some reason.

For Terminal-based software, though, unfortunately it is common, as it's just another bit of UNIX software.