In the hands of a good instructor that freedom is great. Unfortunately, that only applies to those that are better than average, which will not be the majority. By scripting the training they, the certifing organizations, have much better odds of delivering consistent training across the board -- no heros required. If we conducted a poll of instructors and asked to rate themselves how may do you think would rate them selves as average or worse below average?
Being a newbie, I had no way to evaluate the quality of instruction when the instructor went outside the box. One of the reasons I choose PADI was that they maintain strict control over what is taught. I could be realitively assured that I would get consistant training even if I made an error in judgement when selecting my instructor.
I would think that teaching outside of the box would be much more beneficial for more advanced training. It would also be easier for the student to evaluate. During OW the concepts are too new for a newbie evaluate what is good and what isn't.
Just my $.02.