I have noticed when I open the drivers door that water drips quickly out of the drain holes on the underside of the door.

So there is a build up of water within the door which vents on opening the door.

That is what they are designed for, but other doors don't have the same quantity of water dripping out when I open those doors, only a few drips.

So is it the window seal at the base of the window leaking?

Or are there checks I can do to identify the source?

That is how they are, how they have always been.   Remember and unblock the drain holes occasionally.

The issue is when the water does not come out, builds up and eventually there is lots in there.

Remember and open the passengers door winter time if there are hours, days of freezing but occasionally thaws.  You get blocks of ice in there.

 

Skoda have the same thing across different models and even with Mk3, Fabia and likely even with Mk4.

 

The other thing is the design that might have the fuel flap freeze closed on you.