1 - If your son is seen as a starter, then you're going to be sailing against the wind of accepted baseball knowledge (even if it's wrong) to try to convince seasoned baseball guys that a SP shouldn't pitch from the windup with the bases empty. If you listen to our local future HOF MLB broadcasters, they are always talking about getting the opposing pitcher into the stretch.
2 - 1 short ASMI study and 1 Fan Graphs piece are hardly definitive.
3 - There could be any number of other factors not covered in either piece. For example from a comment on the Fan Graphs article: "My take would be that it’s more tiring to pitch from the stretch. Essentially the pitcher has to do the same amount of work to accelerate the baseball in much less time. Hence more power (work/time) is needed. Physiologically, this is more taxing since a higher level of muscle recruitment is needed."
4 - Agree on only teaching LL pitchers one motion, and it's true that the stretch is simpler. But a HS player is different. If he were my kid I'd encourage him to try working on the windup, though not use it in games for now.
(Just a fan/dad's opinion, not expert)