its because turbochargin multiplies air and the stock charger is no longer being fed air by atmospheric pressure. The compressed air being fed through the comp housing of the stock charger is not actually being created by the stock charger. And yes the efficiency of the stock charger goes down as it will not create as much boost as it could by itself.
It is more important to look at the efficiency of the system as a whole. Additionally, we were discussing the flow path of the big charger being obstructed (read: restricted) by the compressor cover of the small charger, that is all.