The main reason that the quiz level setting of "Shuffle Answers" doesn't trickle down to the questions and change the "Shuffle Choices" setting, is that questions can be from Item Banks in the New Quiz, and if the "Shuffle Choices" option was automatically enabled when the "Shuffle Answers" option was enabled, then it would change the settings on Item Banks questions--which you normally wouldn't want to do because it can effect the behavior of the question in all the New Quizzes where the question exists.

If you don't want to shuffle the answer choices for all the questions on the quiz, you will need to manually select which questions that you want the shuffling to occur for.