At least with Linux the distro-specific packages install software where it should go.
On Windows you end up with 32-bit binaries in the 64-bit Program Files folder, and vise versa. You end up with files saved arbitrarily to three different application data directories, and sometimes your Documents folder, so sometimes the registry, why not? Should we put several folders full of drivers directly on the root of the C drive? Of course, where else would they go?