If it was completely controllable, I’d have the ability to control where they are and put them out of my way. Lazy programmers use home as a default.

Home directories have become the *nix version of the Windows Registry.

Very likely you do have the control. You simply haven't taken the time to learn how to configure things.

Or not likely at all, since the whole point of TFA is that many popular programs do not follow specifications and user configuration.

Quite a few applications still have their config path hardcoded.

https://wiki.archlinux.org/index.php/XDG_Base_Directory_supp...

Just because it is designed that way doesn't mean the design isn't a problem.