There is a lot written about mechanics, pitch counts, etc, etc, etc, and a lot of it is contradictory...in fact, for every sound opinion from an expert, you can probably find a sound contrarian opinion from an expert.
You may be on to something when you reference changes to a kids natural motion, I don't know.
My son had labrum surgery and as a power pitcher came back to beat the 18% odds of full rehabilitation to former velocity. He then tore his UCL and one expert he saw, Mets team Dr. Altchek, thought that his shoulder was overly tight and that may have contributed to the elbow injury.
In looking back, I can think of one thing I would have focused more on if I had to do it over again. Maximum development of the decelerator muscles in the back. So much of my research has come back to pointing squarely at the arms ability to safely decelerate, that I think that if you do that, you've focused on that, you've taken the largest step you can to arm injury prevention.
JMHO and I hope for nothing but the best for your son in the future.
Chip