It's all about the training, gents. The training. Training a habit pattern.
Gear up. Pumps off. Cowl flaps closed on level off.
Gear down. Pumps on. Cowl flaps as appropriate.
'Round and 'round the pattern repeating those moves until they are automatic.
Sure, once you have the automaticity drilled in, then you can, and should, begin to think about each movement, and tailor to the specific environment.
Most people, however, barely get enough training time in a complex or multi to go beyound the rote automatic to think or get into the "other than checkride stuff'.
If you were trained initially in a retract, and your instructor/ airplane owner wanted to save wear & tear on the gear and made you do the patterns INITIALLY leaving the gear down all the time, you would be set up to land gear up later when you were PIC and had actally raised the gear.
And experience teaches us that doing a critical motion just a few times may not be enough to really drill it in. Of course this varies with each individual. Do you want to bet your life on being able to "remember".
Don't you think it is better to over-do than under-do?
Training. That's all it is.