Yes they do. Scriptwriters are wage slaves who get overruled constantly by their higher ups, especially capricious directors or even producers (just ask Harlan Ellison about that one). The script writer, even the head writer could pass in the script to the director and by the time it made it through storyboarding it might barely resemble what was originally written as (or , as in GSD, the head writer is the director's wife and rewrites them to her own whims). And even those storyboarded alterations might wind up different still by the time the finished product is done.
Mizushima especially is known as a director who doesn't feel obligated to follow the scripts handed to him to the letter.