As the immobiliser actually communicates with ECU it cannot simply be bypassed (a code is transmitted).
If you cannot retrieve the 4 digit PIN and VW won't give you a 6 digit one you can buy one off ebay that has a pin and then code this to the new key and ecu. VW should give you the 6 digit pin if you give the immobiliser ID (imho 14 digit alphanumeric code)
As I also put in PM, you can change the small brass tumbler things in the lock / or look up the codes on them and should be able to get a key with that.
Alternative, get a set of keys, door handles and coded immo of ebay, then it won't need recoding (you will only need to re-pair with ecu)