Hi scheater5,
I see your dilemma, a possible fix would be to have the index numbers independently sortable from the program numbers. Then you could have list orders that were different from your program number dependent bindings. As far as the difference between the Program by and Program With binding choices the Program by allows continuous controller absolute values if you use a MIDI input type of that sort
or if it is set to a no edge input it can pick an explicit program number.
The Program with binding assumes it is a momentary no edge input and defaults to that when you select it and provides a sandwich menu with the current set-list program numbers and the song they are associated with for your selection.
Maybe @brad will consider this discussion and see a helpful fix or method to help you out. I would vote for it!
Dave