Recommendations and 'guidance' are all very well and some operators will take these on board.
But there are plenty of others that won't. When training is too cost-driven or time-driven, pilots will only get the bare minimum to pass a type rating or check ride.
It is really up to regulators to come out and specify mandatory minimum times to be allocated to manual flight at each stage of training and checking. They already set minimum times for type ratings, line training etc
The FAA says they don't need to see operators specify a minimum amount of manual flying on the line, but why not? We have a minimum number of instrument approaches in 90 day periods etc. Surely in most operations it would be possible for pilots to fit in an hour a month without using the automatics?
There was a a time not that long ago when we had very basic automation. By today's standards the early jets with no autothrottle and limited vertical modes would be seen as a handful, yet they were actually flown very safely in some demanding conditions by quite normal pilots. Manual flying raw data is not that bloody hard ....unless you don't practice.