Crooked,
I'm also the parent of a pitcher who had growth plate-related issues at age 13-14. My son is 16 now. He never got to the point that his arm needed to be put in a cast, and (like most kids I know of) was OK once he got through the years when he was growing really fast. Ages 13-14 are often tough years.
Like you, I don't claim any particular expertise. I did a lot of research--read everything I could find, talked with physical therapists, coaches and doctors. My considered opinion is no one knows the "right" way to pitch (if there is a right way). Ask three experts for their views on proper mechanics and you will get three different opinions. (To take one example, I vividly recall an MLB.com video in which John Smoltz recommended the same wrist turn you are describing here. I searched for the clip and can't find it, so maybe I'm delusional...)
If you have a PC and physical therapist you like and who seem to be within one of the mainstream opinions on mechanics, then I would stick with their advice.
Now that my son is in HS, I don't get involved. But when he was dealing with growth plate issues I communicated a lot (maybe too much) with his travel team and middle school coaches. At the beginning of each season I made sure the coach knew my son's injury history and what his doctor had said re: pitch counts, etc. I also let coaches know my son was working with a local PC/physical therapist. My son's coaches always put a premium on his arm health. Most coaches will (and if they don't, there is a serious problem).
I told my son to expect to hear different things about pitching from different coaches, and that if an instruction was contrary to his PC/PT's or felt like he was hurting his arm, he should tell his coach or tell me. One good thing about injury at an early age: it makes players more aware of the need to take care of their arms. Almost any change to a pitcher's delivery will feel awkward at first, and some may even lead to muscle soreness. Those are fine--but your son has to be the ultimate authority on what is hurting his arm. (And as noted above, it is possible he shouldn't be pitching at all during his fast-growth years. My son threw very little during ages 13-14.)
There is some very good advice in this thread about how to discuss this issue with your son's coach. The only thing I would add is that you shouldn't let anyone tell you they are the ultimate expert and that you must follow their advice. Don't hesitate to say (in the most tactful way the situation permits): "My son's [orthopedist / PC / physical therapist] recommends X, and that has been working well for him."
My son's coaches know a lot more about baseball than I do, but none of them are M.D.s or physical trainers (and even if they were, they never saw his X-rays or MRI results). Good luck. It's hard to know what's best when parenting a young pitcher.