The external trim strip covering the rear roof pillar to quarter panel join is also a leak hot spot - not sure if the plastic peg sockets shrink or what, but a thorough clean and nice bead of body sealant solved the problem for me. This was after years of trying to locate where the water was coming in, even dusting everything in chalk.
I think my boot leak is maybe coming from there, seem to get dampness up in the back of the wing that then runs down on it's merry way to the spare wheel well, couldn't actually see exactly where it was coming from just up the back of beyond somewhere.