Re: asking directors for another take, yes, he did do that with Spielberg, and with Del Toro (reported by a journalist on a set visit), and with Alan Taylor (mentioned on the commentary). It seems to be his actual working technique - when he was talking about working with Spielberg he said he does it because once the director has a take he is happy with he understands what they want and feels like he can give an even better performance with one more take.
It must have driven people slightly crazy on Crimson Peak, because Del Toro is known for doing lots and lots of takes - 40 or 50, sometimes. Or maybe once you'd done that many 'can we just do one more?' doesn't seem like such a big deal.
I guess MA just didn't quite get his working method.