Stephen,
We have seen a few of these instances over the years. There is possible evidence that some GT/CS's came from the factory this way, we assume by accident. Templates were put on the car to drill the holes in the quarter after the main car was assembled and they may have been mixed up side to side.
The indicator on this car would be to decode the sheet metal date codes and see if this quarter is in a range of the build date and the rest of the sheet metal. If it is, then it is a good possibility that it is original and may have came this way. And to make it even harder just because the date code is a lot older, that does not mean it was not sitting on a shelf in a back room.
Ah the fun.....
Rob