the purpose of box squatting is to break the concentric and eccentric motion into two phases, teach correct squat depth and guarantee you're hitting it, and the activation of the stretch reflex. not eliminate it.
box height #'s aren't whats important, what is important is the #s in relation to your parallel. if you find yourself sitting in the hole too long and not developing the power to get out, use a lower than parallel box. if you find yourself losing it on the way up, a higher box may be more beneficial. otherwise i basically just stick to a parallel box.