Decided to investigate this a bit further and I've come to the conclusion that the upper part of the door seal on the GT has to be one of the stupidest, deliberately ineffective designs ever.
With most cars the door rubbers clamp around the seams joining the outer and inner bodyshell panels together, handily covering the spot welds! The GT is the same along the leading, trailing and bottom edges of the door aperture and then, for some inexplicable reason the design is different along the top and the rubber clips into a plastic trim which is screwed on to the upper edge of the door aperture (8 on the diagram)...
The design has nothing to do with the frameless glass because the rubber could still have been clamped to the bodyshell flange and this trim piece could have been just cosmetic or act as an extra splash guard.
Instead, because of the crazy design the only watertight seal is between this plastic trim and the bodyshell and if even the smallest amount of water gets into the gap between this trim and the metal the door rubber will actually direct the water into
There is a foam seal stuck to the back of the strip but mine seems to have flattened with age which is probably how the water is getting in. Also the foam strip is perforated at several points along its length where the screws that attach the strip (not shown in the diagram incidentally) pierce through, which is a weak point.
So, I've re-attached the trim with a bead of silicone sealant between it and the bodyshell (curiously there is a handy little trough on the inside edge of the trim that looks like it was designed exactly for this purpose!).
Another thing I noticed while doing the job is that the leading-edge screw holding the trim was badly corroded so I took the opportunity to replace it and dab the new one with some rustproofing. Might be an idea for all GT owners to at the very least take a look at that screw (you'll find it by pulling back the door rubber behind where the door mirror mount would rest against when the door is closed.