Ouch, I think this could happen just because Fedora doesn't set a
default value of xdg variables. So when some program sees that
XDG_DATA_DIRS is set, it doesn't use /usr/share anymore. So the problem
you faced will probably be fixed if you also append /usr/share to
XDG_DATA_DIRS. I would do it like this:
# Set XDG variables to default values if needed.
[ ! -v XDG_DATA_DIRS ] && [ -d /usr/share ] && export XDG_DATA_DIRS=/usr/share
[ ! -v XDG_CONFIG_DIRS ] && [ -d /etc/xdg ] && export XDG_CONFIG_DIRS=/etc/xdg
export XDG_DATA_DIRS="$HOME/.guix-profile/share:$XDG_DATA_DIRS"