Shoes are at least as personal as saddles. What suits one person will be hell for another.
A good bike fit might suggest a change of SHAPE of shoe (sole shape and stiffness, width of last etc) after a fit, even sometimes when the sole fittings don't allow for the cleat to be in the right place.
However, it's far more usual for the bike fit to suggest a different insole (to allow for arch height, orientation etc), and the best bike fits often include custom foot beds.
I know that some on here rate the Bike Whisperer, but personally I'd question why someone can decide what shoes you should be using before the consultation.