In my opinion OneNote files work better in basic document libraries that don't have versioning or anything else turned on. OneNote handles its own version history and other things related to Office Web Apps when users use it in the browser or sync it to their client applications. From my experience OneNote files just don't work well with the SharePoint version history, library columns etc.
I also encourage or remind users that OneNote it is simply a notebook for taking notes and that official documentation belongs in other places such as word docs etc.
If you compare the other locations OneNote Notebooks can be stored such as a hard drive, network drive, or cloud storage such as OneDrive they by default don't have versioning or columns like SharePoint can so that is why I choose to make the storage places in SharePoint the same if possible.
If you do make a new NoteBook in another library be sure to inform your users to disconnect(right click > close) and re-connect(open from new location on SharePoint) the notebook when it moves from one location to another as it will bread the synced connection in their OneNote client applications. I typically use the client application to connect, disconnect, and move sections/pages around.