Seems to be primarily a Qubes question that belongs to Qubes support. As per What to post in this Qubes-Whonix forum and what not.
The VM auto start logic is up to Qubes dom0.
Would be useful to add some references / links.
Missing Qubes security updates?
On the Whonix side, updating the Templates should be sufficient. There was no need for any security fixes in qubes-core-admin-addon-whonix ever at time of writing. (If there was, check git history for actual changes made in the repository.