There's something about the issueing authority 'Emirate'. If you get an Abu Dhabi visa, you're only allowed to enter/exit through that point.

Once I was redeeming miles with Gulf Air for a trip to Dubai; when I asked for their visa service they told me they could only issue me with a visa to Abu Dhabi, but not to Dubai and in this case my routing has to go into/out of Abu Dhabi.

Again, with Emirates, their transit visa is only good for Dubai Airport.
It could be an airliner thing but I suggest you call the nearest embassy/high comission for UAE and they should be able to help you with this one.

Good luck; let us know how you go.