According to arch wiki, 'only XDG_RUNTIME_DIR is set by default through pam_systemd(8). It is up to the user to explicitly define the other variables according to the specification.'
But in reality, if you check how apps imp XDG spec, most of them just go by following logic without check XDG_RUNTIME_DIR i think.
1. if HOME/.clojure exist, use legacy path
2. else use XFG spec, (or (getenv XDG_CONFIG_HOME) (path HOME/.config/clojure))
XDG_CONFIG_HOME (and the other xdg vars) are unset on most distros, and there are defined defaults that should be used instead. Here's the part clj tools get confused, because it should just write to my HOME/.config/clojure instead of fall back to legacy path.