I think it is a good rule. If a batter was allowed to jump back out of the box when a pitch is being made, it would be distracting to the pitcher.
The keeping one foot in the box is a speed up rule put in place many years ago. It is currently a rule in college. If a batter keeps stepping out of the box in between pitches, I just quietly tell him to stay around the box. If he wants to give me attitude about it, maybe the next close pitch is a strike, just sayin.