Ok, so for future reference (I found the instructions in 
https://www.qubes-os.org/doc/vm-sudo/ to be not completely clear):

The files mentioned in the first part of https://www.qubes-os.org/doc/vm-sudo/, 
namely:

/etc/sudoers.d/qubes
/etc/polkit-1/rules.d/00-qubes-allow-all.rules 
/etc/polkit-1/localauthority/50-local.d/qubes-allow-all.pkla

are to be created/edited in the VM, not in Dom0. This effectively solves the 
problem.

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