Sorry everyone... my house had no electricity for most of today and at work I had to do some... well you know, work
Anyway, the simpler nubbin controller comes with the visual boost 6.5 inch screen and is actually shown in the paper brochure (page 35). I remember it from a demostrator car... it's like a joystick but you can also twiddle it around (between thumb and finger for example) for selecting letters and digits. It basically does everything the other one does except for drawing in things on the top surface.
The larger touch sensitive controller comes with the media XL 8.8 inch screen. I tried very hard to find out whether navigation could do everything that navigation XL could do... I think with XL you can get a 3D view. The main thing that persuaded me was the split screen view you can have with media XL.
I've never really looked at this bit of the manual (pages 19 and 21)... it lookes like you can set the touch pad to control the interactive map... panning and pinch zooming... that sounds quite good, as an alternative to letter and number recognition.
So, for the original question... I think the controller you get depends on the screen size and is independent of whether you have navigation.
If you have visual boost radio and no navigation then you still use the controller for operating the menus... radio, multimedia, telephone (says the manual...
http://www.miniusa.com/content/dam/...14/2014_MINI_Hardtop_with_Onboard_Monitor.pdf