Golf,
You mentioned your new coach was late to the game, which I am interpreting as hired during this school year. I think this gives you a unique inroad to your son having a conversation with the coach since your son had no idea what type of culture and workout regimen the new coach would bring to the program.
With that in mind, your son could approach the coach with this dilemma as a positive. He could say coach, I'm in a bit of a spot here. Since he didn't know the culture and routine that the new coach would bring, I've been working out on my own outside of school to be make sure I'm ready to compete. In some workouts, your dilemma is arm care and potential over use. He could explain what his his workout routine is outside of school to communicate that he's getting reps in and not just bagging some workouts. Finally, he could state that next season he will dial down his outside workouts(if that is indeed the plan) since he now knows what the new coach expects.
After that conversation, you can see what the coach says to determine your next step.