In the case of this script, it is called with the username as parameter (I haven’t checked from where ^^), the proper fix is to put:
export XDG_CONFIG_HOME=/home/$ALIEN_USER/.config
At line 133 of /usr/sbin/alien-generate-properties.sh
It’s actually what Jolla has done on line 42! They simply forgot to do the same on line 133 
Very nice finding @attah, I confirm too that after doing that and having restarted Android support, all checkboxes are checked! 
The fix is so simple, I hope they can still put it in the 4.0.