If you bought it from them new and have also always had it serviced by them (not to mention all the cars you've bought) then you need to puch much harder for goodwill. Go to VW customer service about it too. All they can say is no.......
They can do better than £3k off.
Personally, I would cancel your order for MK6 GTI and go elsewhere.
Another option is to squeeze them as hard as possible for a parts discount, then get the engine fitted by an indy.