Per this discussion, https://forums.whonix.org/t/fixing-whonix-boot-issue-after-securing-qubes-root-auth/3155/8
Whonix executes sudo commands in non-root startup scripts which causes pop-up auth prompts to appear while Whonix VMs are starting. The problem is partly due to sudo parsing sudoers.d entries in alphabetical order, and some later configs cause earlier ones to get overridden. Adding the right permissions to a lexically 'last' filename resolves the issue.
