Sorry for the off-topic and confusion.
For the system, you need to change the default update qube (Dom0 update qube) to sys-whonix.
qubes-os.org/doc/how-to-install-software-in-dom0/#updating-over-tor
Apps Menu > Qubes Tools > Qubes Global Settings > qube defaults
For the templates, you also need to update the qubes.UpdatesProxy policy.
To do that, in a dom0 terminal, run the following command:
whonix.org/wiki/Qubes/Install#Updates_over_Tor
sudo qubesctl state.sls qvm.updates-via-whonix
For Whonix itself, you have nothing to do, the policies already exist in:
/etc/qubes/policy.d/90-default.policy