Somebody correct me if I'm wrong, but don't these always get placed into ~/.guix-profile/etc/profile Right now mine seems almost identical to the output of guix package --search-paths with the only difference being that the values in that file are prepended to the existing ones. Therefore all you should have to do to ensure you always have the right vars is to just source that file.
I have this in my ~/.profile and as far as I can tell it always gives me any vars that guix tells me to set [[ -f /etc/profile ]] && source /etc/profile [[ -f ${HOME}/.guix-profile/etc/profile ]] && source ${HOME}/.guix-profile/etc/profile