A percentage of ex-mill pilots I work with struggle with mode confusion when disengaging or reinstating automatics and poor hand flying abilities with raw data and visual flying. It's not to the extent of the civilian world where experience levels and training seem to be less than what they were a decade ago and MPL like candidates have zero flight time experience to fall back on. So if some experienced ex-mil pilots struggling I'd suggest this points to airline training system modelling themselves on manufacturer recommended minimums. Airbus is probably a good example.
Having seen a number of airline training systems, by far the best for automated aircraft was starting an endorsement process and building up the automation as the course progresses. Perhaps issues aren't totally eliminated such as mode confusion, but the pilot should have the skills to confidently disengage or engage automation, put the aircraft in its desired state and proceed with the flight phase accordingly.