I reckon that join should be at the top, so probably incorrectly fitted.Looks like you are absolutely correct, l've sealed the Alpine Window and the leak has stopped.
Looking at the seal, it has a join at the lower centre, so water is going to run down the glass, down between the seal and glass, and straight through the small gap where the seal joins.
EDIT
I can't remember which way I fitted mine. I think I'll check tomorrow