Gov,
Your son's high school has a nice problem. I wouldn't read too much into it. It is high school baseball, and your son's coach see things differently than you and others (I'm sure). For 6 years I coached/managed a very successful youth travel team with some very good friends of mine. One was a Varsity high school head coach and we've had discussions about certain kids and where to best play them and bat them. Lots of times we agreed and sometimes we didn't. One position that we disagreed on was SS. We had a kid with a sure glove but only an above average arm. I liked his foot work, hands and gritty attitude. He always charged the ball, took time away from the runner thereby making up for his lack of MPH across the diamond. My coach liked the stronger more athletic type at shortstop that didn't have the same glove skills. I had the final say at the time so I had my guy playing short. Fast forward a couple years later when they reached 13 and 14 years old, my friend was now the Head Coach. He had his guy in their because that is who he wanted. it was a matter of comfort and the style of baseball we each liked to coach. Both went on to make their respective high school teams and play shortstop.
What matters with college coaches are tools not where you play in high school, travel or Legion baseball. It is almost irrelevant and I think it sets the players back because of their inflexible mindset. Have an open mind and go with it now and in the future. I can almost guarantee you that if your son is being recruited as a college SS he'll get an opportunity to win that position as a college freshmen, but he will be at a serious disadvantage to upper classmen possibly without even knowing it. The best he can hope for is to learn another position and get some at-bats. If he can hit, he'll get a chance to win that SS position in the future. That has been my experience watching these things over the years.....just my two cents.