Thanks, that's what I was afraid of. I don't really know the best way to go about filling it. If the rear window wasn't already in and sealed, I'd weld the hole up and grind it back down. Since it's in place, I'm afraid to weld around the window, even if I lay something over it. However, the hole is too big to try to fill with seam sealer or body filler. I really don't want to leave it uncovered, as again, I think it's contributing to the water leak in the trunk.
I meant to mention it earlier, though I'm not sure it matters: this is a Metuchen car, built December 8th, 1966.