My S3 hood is water tight except for the top of the doors, and a bit round the quarter light junctions. A bit of water comes in and dribbles down onto the sills. In really heavy rain over a long period this is a real pain, but the car is a LOT more water-tight than it was when delivered and adjusted after several goes by the dealer.
It was quite ridiculous at that stage and I was not a happy bunny!
But the experience was very poor and many new owners (this was my first Morgan) would have given up...
I had heard that hard-tops needed a lot of fiddling to get a good fit, but sounds like this can be done.