Is the seal in contact with the entire trunk opening, or are there any voids where the seal is not being compressed....if so, maybe the seal could be carefully "relieved" with an exacto, where the interference is greatest?
Maybe "shapes" could be cut out of inconspicuous areas or on the backside of the seal to help it compress.
I had the same problem on a coupe trunk, but I was using a reproduction trunklid and seal. So I did not want to spend any more time trying to fight an up-hill-battle. I tweaked the lid and adjusted the latch so it closed without bouncing and sent the car on its way.