Are both sets of skills being mastered during training? 'Cause they're not the same skills!
I don't know about general aviation piloting skills, but both set of skills are certainly not mastered in airline training. Observe any type rating in an airline simulator and you will see that at least 80% is on full use of automation. There are many well known international airlines where manual raw data practice ILS even in fine weather is actively discouraged. Even turning off the flight director in fine weather is considered by some managements as a mortal sin.
A typical airline type instrument rating in Australia is 90% automatics although the rules say "at least one instrument approach must be flown without the autopilot or flight director." If regulators were serious about the potential dangers of automation addiction instead of simply paying lip service, they would require that 50% of the test should be manually flown. Unfortunately that would probably result in a high rate of failures and that costs money.
