Ya creating more flexibility in an athlete is always a good place to start if you want to see quick results. Too many kids don't warm-up properly resulting in both injury, and lower performance levels. It sounds like your trainer is taking a good approach. You need to have a certain level of flexibility to do many exercises, many of which this trainer will probably have your son doing.
So to answer your question, yes becoming more flexible will have a direct effect on performance enhancement. However, creating more flexibility throughout the weeks will also broaden his training opportunity.