Next version of Whonix might include an auto updater.
In any case, it will be made as easy as possible to disable it.
At the moment its enabled by default.
With enough feedback I could get talked into leaving it disabled by default and only notify about updates and then letting people enable it.
Please also leave feedback, if you think it's fine as it stands and should be enabled by default.
The documentation for next Whonix version is here:
I tried to be as verbose as possible for any security implications as possible. Tell me, in case the documentation lacks something.
The whonix_repository man page is here:
The related git code commit is here: