I followed the instructions on Qubes OS to add a GUI prompt for root, it looks like it works fine despite the documentation being outdated. Some of the files to edit and remove are no longer present at all ← unrelated.
I now get the prompt at boot mentioned at the bottom of the page, I created the file /etc/sudoers.d/zz99 and I still got it. I tried changing whonixcheck to systemcheck as I believe it changed name, still got it. How would I prevent this from happening at present time?
At time of writing this isn’t officially supported by Qubes. Quote:
Replacing passwordless root access with Dom0 user prompt
While ITL supports the statement above, some Qubes users may wish to enable user/root isolation in VMs anyway. We do not support it in any of our packages, but of course nothing is preventing the user from modifying his or her own system. A list of steps to do so is provided here without any guarantee of safety, accuracy, or completeness. Proceed at your own risk. Do not rely on this for extra security.