Presumably any logging of instrument flight time must have been hand flying and not flight on automatic pilot.
Not at all. Logging of instrument flight time refers to conditions of flight: simulated, or instrument.
The PIC of a flight may log PIC while the F/O is flying, and may log instrument time for that portion of the flight when the aircraft is operated in instrument conditions or by reference to instruments.
I've found in some aircraft that my biggest challenge isn't hand flying, but operating the aircraft through the automation. I found, for example, that my tendency in the simulator in one aircraft was to disconnect the autopilot and hand-fly, and my difficulty was doing everything through the aircraft systems.
Being proficient at both is important.