LOMCEVAK
The 'conditioning' you refer to is algorithmic learning - gained from demonstration by an instructor and reinforced by lots of practice.
It is a very powerful method of learning and the inevitable downside is that it is difficult to 'unlearn' at a later date, meaning that regression to prior learning, under stress, is a highly probable outcome when using a new system that requires different algorithmic responses.
David Beatty talks (in the Naked Pilot) about the transition issues experienced when BOAC moved from the Comet to the 707 (different landing techniques) and this is a perfect example of the syndrome.
In the most extreme of circumstances, regression can be fatal - so thank goodness that the control systems are mainly standardised as you say.