Certainly some airplane's cockpits were designed better than others to promote flow. Using the Cessnas for example, those from the late 50's were horribly scattered, I opine simply because our industry had not yet come to demand commonality. Standardization can be seen evolving into cockpit design as subsequent design standards improved their definition of the relationship of some controls and instruments to each other. When I was being trained in the Cessna Caravan, it was very evident that it was designed to promote flows, as the required actions and checks corresponded well to slowly sweeping one's hand in several logical directions at each phase of flight. Even flight manuals have evolved over the decades to be standardized. In the mid 1970's manufacturer's agreed on a standardized format, which is now a specified format, so the pilot can learned that certain sections will always
My quick review of the earliest and latest FAR Part 23.777 shows that the earliest, is 8 lines of standard, and the latest is 38 lines. Both define the position of flap control (right of engine controls) and gear (left of engine control), though the latest standard goes much further to define things, for example the relative position of engine controls for centerline thrust aircraft.
And important reason for type training, even if your license covers the new type anyway, may be be differences in the new type, which are not intuitive. I remember being trained in the Cessna 340 after flying the Aztec; a difference, if you suspect an engine fire, to confirm before securing the engine, open the cowl flaps and look, as unlike the Aztec, the 340 (as some other Cessna twins) have cowl flaps on top of the nacelle, rather than underneath, where you may not see the fire exiting the cowl flap.
I remember during my design review of the Lycoming 360 powered DA-42 for it's STC approval, I noticed that Diamond had used the control common to the DA-40 alternate air control for emergency landing gear extension on the DA-42-L360. I commented that DA-40 pilots transitioning to the DA-42 might inadvertently lower the DA-42 gear, while thinking that alternate air was needed. I remember a few DHC-6 Twin Otter landplanes having landing gear selectors installed at the request of the operator, as all of the rest of their fleet were retractable, and they wanted common procedures for all of the aircraft.