Yes, at least in the '09 Eos, the factory iPod option replaces the 3.5mm aux-in (MP3) jack in the armrest console. The iPod adapter has a slot inside the console for your iPod, but you can't access the iPod once it's in place. From what I've read and evolvingpowercat confirms, iPod owners aren't too happy with its limited functionality. The reason it's such a kludge is because all VW did was spoof the head unit into thinking it had a CD changer connected. My wife and I have generic MP3 players, so I removed the unwanted iPod adapter that came on our Eos and replaced it with a Blitzsafe aux-in adapter.I have the standard radio, and am using the MPS input jack with my ipod for now. It works OK, but you have to use the controls on the ipod to start/stop/select playlists, etc.
My understanding is that if I had bought the $200 VW ipod option, I would lose the universal MP3 input and instead get a dedicated ipod connection. I think that means that data as wellas music would go the radio, so the song/artist info woudl be displayed, as well giving me the ability to change playlists....? Is that correct? If so, it might we worth going back to the dealer.