To be honest, I very much like the xorg.conf.d-way it currently has. I think the current way is by far the best.

You don't really want a dependency of libxwiimote to XDG_CONFIG_HOME/XDG_CONFIG_DIR (the latter would be /etc btw), as application should do this.
And you don't really want xf-input-drivers messing around with config-files eather.