This sounds like poor communication from either or both, motability and the dealer/audi. You have a contract signed for a specific car spec at an agreed price. You’re not party to car availability on the scheme, that’s motability and audi.
If the car had an increase in AP then you should have been informed, when it came into force. Not upon collection, I can imagine the embarrassment you faced when you were asked to stump up another £1k. This isn’t a few pounds, a grand is a lot of money. Is it possible that when the order went through, the updated price on motability changed ? Either way I wouldn’t stand for it and I can’t believe Motabilities stance with you either!