User blog comment:Rhiabloom12/Evils Kingdom Booklet/@comment-6966973-20130313070335/@comment-4418534-20130408213841

To clarify the black box it is reffering to the chest in Twiright Prank. Now yes, the black room where Irregular is is the closest reference to it in the song it is in the description for. We must then conclude they are the same.

This would mean that Irregular/Allen's soul is yes in the box. We also know they are in the Director Doll. So Irregular is in the box which is then made into theDirector Doll.

It has been said that Irena Clockworker (as Julia Abelard) most likely made the clockwork doll/ the Director Doll. She then gave it to  Margarita Blankenheim. The logical conclusion is that Irena at one point went back to the beach (she was behind the Twiright Prank inncident)and obtained the black box/chest which she later made into the clockwork doll/Doll Director.

I am not sure if she was aware of  Irregular/Allen's soul pressence but that is my understanding without making far fetched ideas.