Agreed... ultimately, the total air intake is decided by the intake valve size. So if you have oversized valves, as one of my motors does, your values and experiences may vary.
But, gutted intake, stock intake or MWR XXL intake, the characteristics as to how much and to what degree the airbox will pressurize, changes. Those changes throw of the "set values" the ECU is programmed with that automatically compensate with fuel as the bike is designed with those "set values" in mind. So when you change how fast or the amount of pressure the airbox sees, those set values the compensation maps are designed off of are no longer valid.