Batman, Inc. was allowed to continue only to keep Morrison happy by letting him finish his story. He's leaving soon...
My guess is that a lot of elements from his run and from Inc. will be ignored in the future and not be refer to again.
When one reads Inc. it's clear that you'll need the previous continuity for it to make sense. That ship has sailed.
My advice is to enjoy it for what it is, Morrison's swan song. That era is over, we're moving forward!