Many of the personal recollections / incidents relate to incorrect switching or mode awareness. Switching the FD off should avoid these ‘errors’, but the subsequent manual flight may not help pilots avoid similar problems of switching / awareness where FD or autopilot use is essential; particularly if these are the same issues which the FAA SAFO recommendation refers too (#1).
More manual instrument flight should reinforce skills of scanning and awareness, but its effectiveness will depend on the flight situations encountered. The more demanding tasks (flight-path precision, high workload, mental awareness) during departure or approach are unlikely to be hand flown, nor without FD. This conflict results from the increasing complexity of modern operations, and in what is required or expected of pilots in order to be efficient (but not at the expense of safety).
The recollections / incidents also indicate ineffective cross monitoring. Does the PM check manual flight accuracy with respect to the FD, or in autoflight does the crew rate the autopilot performance according to the FD. Only the aircraft instruments show what is happening (now) vs the FD which indicates what has been selected to happen (future); we shouldn’t check 'now' based on thoughts of the future.
These are potentially hazardous behaviours which may overlook selection mistakes or mode transitions; also they may result in a poor understanding of where the aircraft is going or what the system is attempting to accomplish. These ‘errors’ may be independent of manual flight skills in benign situations.
Monitoring - Plane, Path, People (and self), requires knowledge of a norm, what has been planned, expected, of what is important, and how and when to check a parameter.
This involves discipline, the habit of scanning and comparing via understanding:- what is happening vs what is required. Many of the apparent problems of automatic and manual flight are actually in this understanding.