An overlayed ebook reader icon would most likely work better than both a 1px border or another background color. It would be more obvious.
With the new database backend I would suspect that it might soon become possible to have more than one instance of calibre running at once? That would enable you to have more than one "real" library open at the same time.
Then after that all that is needed is "just" to implement drag-and-drop and copy-paste between instances.