Just was starting to write a bug report for this when I saw your post. I really wonder if this is by design. And I can not imagine what it would be useful for in the CC backend?!
For me it is very annoying because I cannot determine if the Inner Blocks element is ampty or not on the frontend. Since the div gets replaced if you add a block you cannot tell if the div was added by the user or by CC. @Louis, @Araminta, if it is necessary in the backend I would appreciate if it could be marked with a class or something so that I can differentiate it on the frontend.