First of all, the larger the injector, the slower rate it opens and closes, due to the higher volume of exiting fuel. Thus making a larger injector noisier, and if the injector is opening at a slower rate this will definately have a direct effect on how fast the injector can respond to immediate changes in throttle position. Obviously, you have somewhat of an understanding of this, by the fact that you typed (to a certain extent). A change in the size of injector, period, will in turn affect that particular engine's ability to respond quickly, to change.
As well, I never said it was an issue, just definately something noticeable, regaurdless of how knowledgeable your tuner is.

And for the issue of an injector coming from the factory at 100% duty cycle. I am definately not confused, an Integra gsr, factory settings, at 0.8" of MAP pressure at 8525 rpm, the factory injectors are at 100% duty cycle. The higher the cycle you run a specific injector, the better the spray pattern gets, considering you are reaching it's maximum recomended cycle.