No, P-Tronic box-units are regulated so that they maintain vehicles at the combustion norms in application within the car industry. Your car will neither smoke nor pollute more. But the decrease in fuel consumption brought about by the box-unit will also be the basis for diminishing your noxious emissions. It is logical - if you consume less, you pollute less.
It is quite common, though, to be overtaken by speed merchants - whose power has clearly been increased - followed by a plume of nasty black smoke. In these cases, either the engine has a problem or the reprogramming has been carried out with poor quality equipment.