There is or was an excellent site somewhere on the Net that went into the physics of the free throw and made the case that the best technique was the underhanded or granny shot. I can’t find it right now but here’s one to get you started.
One of the advantages of the underhanded throw is the way that the ball follows a natural arch to the basket and goes in near the top of the arch and thus the point of the least velocity. Tall players will naturally want to throw the ball straight at the basket and must learn to put an artificial arch on the trajectory. Shorter players by necessity will throw with a greater arch and the top of the arch will be nearer the basket, thus less velocity. This could explain the difference.