When it rains no matter how hard, the car is OK and dry. However when cleaning the car, if I throw a bucket of rinse water over the roof, towards the rear, about an hour later I get around 4 little drips of water into the boot tray along a straight line. I have determined that water can creep over the tailgate seal at the top in the area between the 2 sets of hinges. The water enters the gutter, splashes onto the hinges and the actual door inner surface and these water droplets are sitting directly above  the pinch point between seal and tailgate. These drips then fall onto this joint line and work through the seal. Its minimal now but could deteriorate over time. I think the set pins holding the hinges sit in slotted holes and I guess the allows adjustment of the tailgate fit. I have noted this to the dealer who is willing to take the car in for a look see and I will in due course report back on this item. Has anyone else had this problem.

Skoda have struggled with water ingress for years across multiple models.

 

There were lots of different causes but one significant one was the poor drainage of the boot seal. There are small holes at various points to allow water to escape. Unfortunately they were often poorly locatedbpreventing them from draining properly. Slamming the boot would then force the water into the boot at various points.