AF447, Emirates 521, AA 8501, etc. could fly manual just fine. The problem was that they had no idea what the automation was doing when problems crop up.
Well let's look at the Emirates B777 go round from touch down. Do you need a two day course to tell you to push the thrust levers forward if they do not move forward on their own? Or to check the engine gauges to confirm that the engines are spooling up after pressing TOGA? That is fundamental "pilot stuff" surely?
Isn't the point that if " they had no idea what the automation was doing" then they should hand fly? As you say "they could fly manual just fine".
I agree it is not too difficult to occasionally "get lost" in the automation modes, that is why there are disconnect buttons.