Hi,
I'm putting the rear of my Cuda together and am in about the same spot as you, fitting and tweaking. I have an AMD tail panel and decklid (with cutouts if that matters). The tail panel I got did not have the two dings and the 'pressed in' area around the lock. Sounds like your panel slipped past QC, or got mishandled sometime after it left the factory. Probably should have gone back, may be too late now - not sure.
The decklid arch matches the arch of the tail panel. Can't even speculate why yours don't match.
Have you tried bending down the flange on the upper edge of the tail panel so you can see exactly what the gap is? Don't know if that will help, but you can see exactly what the gap is.
I have an issue that I'm trying to figure out how to correct. On my car, the decklid lines up at the corners by the quarters with the tail panel, but the decklid sticks out over the tail panel by about a 1/4 inch in the center. Once you bend that inner flange down, you may run into the same issue. Don't know if it's common. You have enough on your hands, I hope you don't have to deal with my issue too! Here's a pic of what I'm talking about.
Sean