There were 16 or so 289 competition cars built with the wide rear fenders (called "wide wings" by AC) and cut back doors. Of those, only 3 or 4 had a dimpled trunk to accommodate the FIA suitcase (the extra gas tank took up too much room). Interestingly, not all of the cars that competed in FIA events had the dimples and, of course, they would not be needed for USRRC events.
Here are pictures of a Shelby team car at the Targa Florio, an FIA event, with a smooth trunk. It also has the Cobra trunk and nose badge, the "Powered by Ford" badge above the front fender vent, and the gas cap wind deflector:
These two team cars at the same race had trunk dimples; they also did not have any badges or the gas cap wind deflector:
This links to a video from that race, the 1964 Targa Florio, with a lot of footage of the Cobras:
http://www.youtube.com/watch?v=3rRvf...eature=related