Hello, please tell me if there is not such a aperture at your MKV. I show you the aperture through which rain water would come into the room at my MKV by a photo.
When the roof handle is locked the rear of the sliding panel should rise such that the roof has a continuous line. There is still a gap down the sides of the sliding panel but any rain water entering there should be drained away by the rubber drain pipes connected at each of the four corners of the inner tray. If there is leakage into the interior it could be that the drains have become blocked or the rubber pipes perished or possibly the inner tray may have been corroded into holes.
In addition to Peter’s explanation, there should be rubber sealing strips across the front and rear of the sliding roof panel.