Could calamares be configured to somehow not create user user during boot instead? That would simplify implementation on the Whonix side a lot.
Then we might be able to use /usr/share/pam-configs/mkhomedir ( http://blog.dailystuff.nl/2012/07/create-home-directory-on-first-login/ ) which would also solve ⚓ T913 bug: not all files form /etc/skel are copied to /home/user / create user "user" at boot time / bug: not all files form /etc/skel are copied to /home/user - #4 by Patrick.
( sudo pam-auth-update --enable mkhomedir )