I think a lot of it might be comfort factor.
Hey, if you know the guy back there can catch your nastiest slider, you thorw your nastiest slider. If you find yourself watching him chase it to the backstop a couple times, maybe you dial it back a bit.
Also there is the possibilty that it is all prep work. Maybe Catcher A sticks to the game plan better for certain hitters. If the guy at the plate struggles up and in, maybe he executes a better plan to set up an up and in out pitcher better than catcher B.
Those are my theories, and probably not ones I explained very well. It might be easier to give examples of the first, but I can't think of any. For the second, straight up conjecture on my part...