head work and port work and runner alterations change the car's breathing ability and change the CFM rating or how many lb/min the engine can breath... thats how they calcualte Pumping efficiency. if an engine was Perfect, it would breath 3.0 liters of air for every 2 crank revolutions... but due to inherent design flaws, it will only flow LESS than 100% efficiency. Forced induction fixes this problem.
besides, all the design errors,flaws, and limitations can only make the flow rate of the compressor WORSE... the compressor flow rates are measured at the discharge outlet w/ no restrictions. so thats what the compressor wheel COULD flow in a perfect world... if your engine was perfect... like the 7M
or a 2JZ w/ a 1JZ head.