Water will always get through seals like sunroofs and door weather strips, its the drainage that stops the water from entering the car.
Open the sunroof and pour water down the channels and you'll see it rolling away through holes at the front which go down the A-Pillar post. The water should collect at the bottom of each wheel arch. Not like my old Mk2:

Water was clearly coming down from the headlining so I used the softest welding rod to push it down the drain hole to see if it was blocked and initially became very confused! Removed the A post trim and found the drain pipe had come off. Easy fix.
If your drain holes are blocked then use gentle compressed air down the holes to avoid the pipes popping off. As for the seal, if its not split or torn and appears to make a good seal then it probably is stopping more water getting in, its getting the water out that is more likely your problem
Leon