You are right about them not controlling The Masters, but because they recognize it as an official part of the Tour's schedule, and it is an official money event that counts on the PGA Tour and it awards FedEx Cup points, the Tour still has the right to fine him.
I don't believe course management was his problem at the Masters, and we certainly didn't hear a word about course management at API. After all he won it. He knows where he has to hit them and where the good miss is. Face it, he just didn't hit it well at all at the Masters for what ever reason. If you aren't hitting it well, course management sort of goes out the window and you are continually scrambling.
Cussing, club dropping, doesn't bother me. Booting it on the other hand, maybe not.