First let me say I understand the reasoning and it's a good plan, given how many ignore the 'updates'. I only have one qualm about these auto backups: plug-ins. They don't always update fast enough to function under the new version. Sometimes one finds a conflict or bug the hard way and need to go looking for a replacement. That's why I always download a backup before I update even if its a small update.
Therefore I think there should be a control panel to allow for more user control over the updates. Besides just off and on, one could add a time delay option for those who are afraid of forgetting, say a week for instance - to check for plug in updates and compatibility concerns. Just because one wouldn't break or even update the 'core' site doesn't mean it might not look atrocious or lose important functionality when a plug in goes kerblooey over some otherwise minor change. (Been there. Done that.)
It's a bit much to expect a user to go hacking code to turn them off when they have a lot of possibly elderly plug ins. But more control would give one time to look for a replacement and some of the 'slower' plug in updaters time to find bugs. After all, some of them are working for free.