I dont think you will have a problem using the different barrels as they are only mechanical.
The coded part clips round the metal housing so as long as you use the corresponding old key chip in the new key you shouldn't have a problem. See the black plastic part around the barrel. Thats the coded part to the key. Again picture from a Seat Ibiza but is the same in the mk3 Golf.

To drill that hole to release the barrel you won't be able to drill it with the barrel housing still in the car.