The pitcher can call off the catcher, correct.
If you have a veteran catcher like Matt was, and a younger pitcher a little wet behind the ears, shake the catcher off, too much, then I am not surprise when the mask comes off, the catcher calls time, and visits the mound, to remind the pitcher, whose the boss on the field.
Now, if its a veteran pitcher like Mussina, yes, you are control, he pretty much threw what he wanted to.