I think the confusion is between "Over-ride" and "Disconnect". I don't think AB is saying don't disconnect or downgrade automation if it isn't delivering what is required- but don't OVER-RIDE that is, make manual inputs while the automation is still connected, unless it's a serious, time critical problem.
In a Boeing, the same would be true of the A/P, though there's no problem "Helping" the A/T a bit if it is slow correcting the speed.