Just been along to the dealer. It just so happened that the Arnold Clark warranty guy for this area was in at the time. Both him and the service manager came out to look at it. The warranty guy seems to think that the surface of the paint has been damaged and this has allowed the moisture to get in

I tried to point out that the bubble on the other side is actually under the edge of the glass so how could the paint get chipped or damaged? He didnt really have an answer for this.
He said i've now got 2 options, get this,
"As a gesture of good will we will put it down as a paint defect and get the boot repainted" I asked if they would replace the tailgate and he said no, they wont even take the window out!!
or
"We can get an independant paint inspector to come in and look at it and give his opinion on what has caused it"They then tried to put the wind up me at this point by saying that if he says the rust is a result of the paint being damaged i wont be entitiled to a warranty claim

I told them to go ahead and get the inspector out as I dont believe for a second that this is a result of the surface of the paint being damaged.
For paint damage to cause rust it would need to go through the lacquer, base coat, primer and then through the galvanised coating and expose bare steel, some how i dont think so.
I'm just off the phone to VW customer services, the guy i spoke to seemed pretty good about it and didnt immediately rule out the possibilty of being able to reject the car. Need to wait for the guy who's going to be dealing with the case to call me back, we'll see what he says.
Are you sure that is a rust spot in the first picture because it looks more like a blob of molten metal. Not to start a panic but its like blob from a body repair with a stud welder
The pictures were taken in macro so the raised bit in the first picture does look a bit like something poking through the paint but i think it's just the way the rust is pushing through.
Could you pop the trim off the inside of the tailgate and see if there's been some repair work done to the metal? That shouldn't happen.
I've not taken the trim off, dont want to touch anything just now. Going to wait till this inspector has a look and i hear back from VW before i do anything.