Pazz if you have the correct arm-rest I would just go for the MDI in that location as you will then be able to secure the ipod in the cubby hole, if not the standard MDI retro for the glove box would involve less work than retro-fitting the shelf and MDI.
My guess is that the part Camel found in ETKA is for cars that didnt have the arm-rest cubby hole before they bought out the MDI only unit. And for Passat owners who wanted to replace their 6 CD units.