Just curious ... why would you have to maintain 3*N build systems? The apps could share source trees, bug reporting, and any overhead?
Simply segmenting the python code by app and sharing a central library should work from a build perspective for separate apps, wouldn't it?
The UI for the library could then be greatly streamlined which should improve performance, and the cli ebook-tools could become standalone, batch oriented, and pipe-able. You could then do conversion by simple drag and dropping into a "watched" conversion folder.
You could even assign developers based on the main functionality of the apps - you do something similar for the ebook input/output drivers anyway, right?
I guess I am just a big fan of the old unix philosophy of small focused programs that do one thing and do it really well.
Calibre does do things really well but much of its feature set may be overkill for many users.
As I said ... its just a thought.