I'm not sure what's complicated here - Sunao and Shuuya discovered they can make replicas separately to do the things they don't want to do/be responsible for.
Sunao for the exercise, the tests, the apologies, etc, Shuuya for the purpose of wallowing in his self pity.
Shuuya, wallowing, hatched a plan where he wants to go one place while his Replica beats up the guy who hurt him, his replica just happened to tell Sunao's Replica. She - completely separate from her, "owner" I guess, is going to be pulled into the plot.
All that aside, I wonder if the Replicas never went back home, could they be dismissed or would they be able to continue to exist. I mean, besides not having shelter, food or money.