I don't get the problem. Why bother where dotfiles are written to? GUI file managers and userland tools hide them by default. What would I gain by having them written outside of $HOME?
Home directory is the default directory for terminal emulators, and having it polluted to me feels like sitting in a dirty room.
My comment wasn't meant as a criticism of the basic idea of a standard directory scheme; it was a reply to someone asking why anyone would ever care about files you can't see.
~/.cache can burn, though:)
So I guess if any of your applications have important data, you better back it up! (I learned today)
* My definition of "garbage" in this context is stuff I don't miss if I wipe the machine, reinstall the OS and the app, and sign in again.