Over my career I have run both styles,sometimes for the same employer with Cat excavators and John Deere backhoes.It was never a problem adjusting to either style and I didn't even think about it,it became routine for me.
The problem seems to be when you stay with one style for a period of time there is a slight readjustment needed to become comfortable with the other one.
I worked for one company that had the same equipment but had changed the backhoe to the Cat pattern,that threw me for a few minutes.
It seems like the rubber tires was the trigger that put me in whatever mode I had to be in to make it work.
I prefer the Cat configuration as it seems to be the predominant one in this area but I feel that the John Deere style is more "intuitive",that is to say that if a person with no experience on either style were to learn it from the beginning that the John Deere would be the easiest to become proficient on.
I once applied for a job as an operator running the Cat configuration after running a Hitachi with the JD setup for several months,that was fun.They hired me anyway.
Ron G