Let’s answer the OP’s question. Are auto updates a problem?
The problem with auto updates is that if the update is broken. Tor (as well as many others) have released updates that break things in unexpected ways. Personally, I never update right away for this reason. I like to let other people be the test subjects and see what happens.
Personally, I went right into Tor and turned auto updates off. Which, of course, is itself a problem because it can be tracked.
Before Patrick removes the update check feature in Whonix I’d suggest he go back and read his own warning message and consider anew why that warning message is there. There is an excellent reason why the warning messages says that if there are multiple versions of Tor to be updated too it’s best to pick the lowest version on the list–it’s likely to be the most stable.
I’m not happy that Tor has chosen to go down this road. I think it is a mistake. But there it is.