It can help the training process to have a young horse stalled, because getting worked becomes something they look forward to. They get out of the boring stall for a training session. It also helps him learn to rely on his trainer to be his leader, if he is not turned out with other horses who can fill that role. So you develop a horse with a good work ethic that views you as his leader. Horses need to learn alot of things to be useful, stalling a horse during training can speed up a couple of important ones.