apt full-upgrade ?
--no-install-recommends ?
Look why, maybe add them manually ? Check dependencies with apt-cache showpkg.
man apt-get has many solutions.
You can use --dry-run (even as user) to see what apt will do, w/o doing it.
Or, as the instructions are for 4.0, and you posted in 4.1, things have changed in the template.
But IMO, it looks like a standard Debian testing/Kali problem, nothing really Qubes related.