Marvel pretty much does the same but their movies are always in crunch time, difficult decisions being made with the clock ticking, AOU didn't come out unscathed.
Yes, I do recall the Thor 2 guy saying that Marvel pretty much let him do whatever he wanted during filming but then in the editing room they took over and made a completely different movie than what he was envisioning. With AoU at least Disney was saying things like "lets lose 10 minutes of farmhouse please," not "lets lose 10 minutes of THOR. He sucks. More Tony Stark. He's cool. We don't care about how it affects the story, just film him doing whatever."