In the Amsterdam and S. Francisco cases, no one noticed the developing upset situation. We can not compare, what is not comparable...
Exactly what happened in southern Atlantic, in the Java Sea, in Buffalo, ..., a crew not noticing what is happening.
In the bus, with unconnected side-sticks, the PM is only able to see aircraft reactions (to the PF inputs), not the actions that led to those reactions, and this fact makes all the difference...
Reacting to aircraft reactions is what basic flying is, at least where I fly. By applying pitch and power, using engine instruments and artificial horizon, controlling the result on ASI, HDG, VSI etc. TL angle or yoke position are not part of this control loop.
Is it a regular practice on normal flights in flight phases with no stress (weather, hurry, ...) to fly with autopilot off, with the intent to keep the feeling for the airplane handling and the routine checks of AOA, speed, horizon, thrust alive?
You don't need to feel your airplane, it is really not that difficult. Just fly the effing plane and don't pull abnormal pitch. It is really not rocket science to do it, if you now what is required. However, knowing what to do seems impossible to a fraction of crews.