SoCalDad,
All of the factors you've noted are an inherent part of the statistics you've quoted. The fact is that most kids won't get enough supervision to avoid doing those things.
If a kid gets enough proper supervision, and his arm is well conditioned then the risk is probably minimized.
I do have concerns that even the best conditioned arms may be susceptible to long term repetitive stress type of injuries in areas that don't heal as quickly as muscle. Something like that would of course depend on the individual. No scientific proof, just a concern. It will be interesting to see how well your son's arm holds up over time. I doubt that many pitchers have thrown so hard so young or have been as well prepared to do so. Hopefully your son's arm will have the durability that Ryan's did.