If your service manager said he thought it was only covered for three years, then this is his thought. It sounds to me like he's guessing.
My point is that if he acknowledges that the item was covered in the original first three years of warranty then to comply with the "....exactly the same....." clause in the extended warranty leaflet the item has to be covered in the extended period. If your service manager can't understand this then I would be getting straight on to VWCS (informing your service manager of your intent) and start giving them a bit of grief. All the best.