This is a dicey situation, but I don't believe it is as simple as "just listen to the coach, and then do what you do". Some coaches could label the kid as "uncoachable", and that is not a label you want your kid to have. What if the coach is asked about your kid? What is coach going to say? Probably not very good things.
Your thoughts may be that this coach is unqualified, but the reality is, that doesn't matter. Word travels fast in baseball, and you don't want your kid to get a bad reputation.
I've found that I have even learned things from people that I didn't consider to be too bright. How? I listened, and by doing so, I was able to gain a different perspective. It may have been what not to do, but I learned from them.
Some of you are saying to "hear" what the coach is saying, but you aren't really telling him to "listen".
I believe you should have the conversation with your coach and have the kid present too. As a parent, his arm health is paramount. During this conversation, you and your son can talk to the coach about what has been prescribed to him, what you have been counseled against, etc.