It wouldn't matter if he misses his connection. As soon as you come through the gates, after stepping off the trams, you will see Magical Express staff members in blue blazers, tan skirts and pants waving the big Mickey Hands. They will direct them to the Magical Express boarding area. So no fears.
Word of advise - have them pack a bag with a change of clothes and toiletries. My husband works the ramp for the airlines and he tells me that the ME bags have the special tags and they are removed off the plane and placed onto a separate container to be transported via truck to the hotels. However, sometimes they sit there for hours and hours.