Its not the drain hole you see when you open your fuel flap. That is where the petrol would go if you didn't stop filling once it had come up to the neck of the filler.
I spoke with the technician who worked on my car as I wasn't that happy about how he had pulled the door into the frame more to stop the outside noise coming in but that's a different story
The way I understood him was, if you open your fuel flap you will see that the plastic shroud isn't sealed to the body of the car. You can move it about slightly. So when its raining and the water is running down the side of your car some is going to make its way into the fuel flap area. Some will drop off and go out through the drainage hole but some will make its way behind the plastic shroud. He told me that's natural and there is a drainage system in there but for some reason mine had been closed over. He never said what with. Probably paint or body sealant. Anyway with that sealed up there was nowhere for the water to go so after it had filled up so far it made its way round to the boot. He said the car has what you could describe as an inner skin and this is usually sealed so nothing can get in but this particular skin compartment had access.
I had an old car a few years back as a run around and every time you braked you could hear what sounded like a bath full of water swishing back and forth
I never did find out where it was as it didn't cause any problems but probably something similar.
