If "Automatically enable all new beta features" is checked in [[Special:Preferences#mw-prefsection-betafeatures]] and you de-enable one or more beta features and save, the features stay enabled.
They do de-enable if you uncheck "Automatically enable all new beta features" but then you miss this feature. I am sure it wasn't working like that.
At this moment it is not enabling all new beta features but all of them.
[copied the better description from merged 186439]