Just using a different method to determine air flow. Instead of direct measurement, it's calculated. The larger throttle bores will make for greater pressure changes with the same throttle movement, so, the PCM IS aware that it's getting more air the previously.

 

As stated speed density is calculated, using primarily air temp and vacuum versus barometric pressure to calculate injector pulse width. When you introduce more air, you cause less manifold vac and so the equation changes and pulse width increases.

If it didn't change, you'd ping like crazy every time you tried to drive above 10% throttle.