sometimes there is more than one track of the same title. Without knowing which playlist each is in (easily) you don't know which one to delete.
It has already been supported for a long time. Once you add your file to CopyTrans Manager, right click on it and select "Edit" (or open it with CTRL+E), then from "Media kind" drop down select Audiobook. After updating your device, the audiobook will be visible in the "Books" app.