Except that Batman, Inc and "Batman" appear to be completely separate entities. We have Leviathan's forces going against Bruce and Damian in that book, and the Court of Owls against them in "Batman". I very much doubt that Morrison would incorporate the Court into the finale of Inc. I get the thematic conflict between the Court and Bruce, it was apparent in the first issue of the book and going all the way back to Gates of Gotham. The ongoing conflict is control over Gotham City.