Nonsense. First of all there is no extra belt length (due to the smaller pulleys) unless you installed a longer belt. There is more slack with smaller pulleys but that's what tensioners are for. The only pulley that can affect the boost of the charger is the one providing the force - that being the crankshaft. It spins at a particular RPM and if you were to install a larger pulley, then the belt would move faster. A belt, unless it's slipping, is no different than if all the pulleys were gears connected together. The only thing that determines how fast the gears spin is how fast the drive gear is spinning and how large it is.
If the belt is not slipping (which would only cause you less boost), if the crank pulley did not change, the charger pulley speed will not either, period. They must have thought you have a smaller crank pulley as well... for whatever reason. That's the only possible explanation I can think of for their logic.