Of course the shop should set any bike up the way the customer wants it, and it's bad form to steer the customer toward a lower end bike just in order to avoid having to change the setup.

On the other hand (as a general point and not specific to the example cited by OP) I can see where an experienced rider/salesman/mechanic might would be quite right to steer an inexperienced customer/rider away from a certain setup idea that they perceive to be more comfortable. Case in point, raising the handlebar and moving it back will change the weight distribution in a way that may be poorly suited to a bike's geometry, and a salesman would be remiss for not pointing this out.