You're likely right. The other places that I've found are the upper corners, where the rear sail is tacked on (just inboard of the hinges), and the seal itself. If the upper part of that seal gets a hole worn into it, water flows into the channel and lets itself into the trunk through several little air perforations on the bottom.
Grab a buddy, a hose, a flashlight and a case of beer. Put the beer in the trunk, get in the trunk with the beer, have your buddy close the trunk & then hose the car down. You'll see the leaks more or less...and your buddy will be properly motivated to let you back out...