People are saying the scene happens in story mode. I believe its a flashback and netherrealm just changed how shinnok got imprisoned. You got to think the old way was raiden banished him to the netherrealm, but in MK9 you have people like quan chi and scorpion come and go from the netherrealm, so why can't he come and go? They probably felt it made more sense to change the backstory a lil bit.