The rear license plate goes on the trunk lid just above the handle. The bottom of the license plate is about 1 inch above the handle. Sounds like somebody must have filled the holes. If you see any cars or pictures of cars with the luggage rack the license plate and the luggage rack are mounted to the same two top bolts. The upper two connection points on this luggage rack are the two hinges. This is so you don't confuse it with the racks that require drilling holes in the trunk. I say all of this just so you will know that there is really a precise location of the two top license plate holes. My TR4 has all four holes drilled.
Good luck.
Charley Fitch