Can't forget to read the chapter "10,000 spirals." Like you are describing, that's where Steve makes it clear he had never been taught to throw a football correctly. He taught himself, then threw thousands of passes to get better.
In this particular case (Steve Young's case), I think the coaches knew what they were talking about. Also, when Steve got better, they moved him up the depth chart. But he didn't play until McMahon got hurt.