2) the pilot flying was inadequately and/or incompletely trained in manual operation the airplane with or without assistance provided by whatever automatic systems
I think the issue is about the "with or without assistance provided" part of this sentence. The pilot thought he would fly the aircraft "with assistance provided" while in fact he was flying it "without assistance provided" (because he unintentionally and unnoticed asked the "assistant" to quit).
All the other issues (adequacy of the instrumentation etc.) are just secondary, the main issue is that the pilot thought he would do something different from what he was actually doing. It was about understanding how to work together with systems. Obviously he was not trained to question what the systems are doing. Obviously he was not trained to monitor the systems. He was trained to trust in the systems.
It is hard to blame any single aspect, but it is easy to identify where everybody can improve (airplane designers, training organisations, pilots, airlines, authorities....), and that is just what we should do now.