How do professional bakers handle rotating trays while mass producing cookies/muffins/cakes/etc.?
Swapping and rotating baking trays is recommended in order to account for differences in temperature inside residential ovens.  Typically, the top of the oven is significantly hotter than the bottom.  This is less of a concern with modern ovens, particularly those with fans to circulate the air (commonly called "convection ovens").  

Professional bakeries will use a professional oven that evenly distributes the heat and/or automatically rotates the trays, thus not requiring manual swapping or rotation of the trays.