If you have read any of the rules for regular missions they specify "Entirely within xx inches" and "Within xxinches". Several psychich powers use "Within xx inches" and deployement uses "within xxinches" and shows the model not being entirely within the area. A vehicle would only have to have it's corner within 3" of the center mark.
Units on transports and their placement in the vehicle has to be worked out with your opponents ahead of time. Since the center point of the vehicle can't work for all embarked troops if there is more than one, you'll have to work it out another way.