Latest mk8 Golf spec and price list brochure is effective 24/09/21, so if your car was registered on or after that date, those prices will be used to determine whether or not your car falls into the luxury VED band.
If your car was registered before 24/09/21 and the list price - ex first reg fee and first year’s VED - was less than £40k (your invoice figure suggests that is the case), then you shouldn’t be liable for the additional luxury VED. In your position, I’d be checking with the dealer to establish the date your car was registered, and if it was before 24/09/21 IMHO you shouldn’t have to pay the additional VED.
Please update the forum with the outcome, once you’ve spoken to your dealer.