Having the dock in the head unit itself takes up a load of valuable space inside the head unit. Also, it adds to the variants massively, requiring more design for each compatible model, meaning it is likely to be on less models.

Having the dock external to the head unit means the interface could be made much more universal and compatible with lots of head units, possibly without mods on some (maybe with reduced functionality).

Then you could keep the CD in the head unit as well, without compromising on performance.

It also means you can cope with different portables (iPod, minipod, or whatever) with a suitable connector and minimal changes.

Nick