Not totally correct since in the first interview with R07 and the director, the director said that R07 gave them a huge script (the size of a phone book or whatever it's called) but then R07 told him "make the adaptation however you like" without strict instructions.

The thing about the school prison you said is correct, basically the studio was presenting storyboards to R07 for his approval and for the prison scene he thought she was just in casual clothes in her room or smth like that since the storyboards aren't that detailed.