I have the same, my dealer has sold me 4 cars previously and done me proud to date really can't fault them so trust completely. £500 is from Audi finance and £500 from dealer. As I already have £4k discount dealer told me I could have lower interest rate and the £500 from Audi UK but could not run to anymore. Overall I am happy as its reduced my overall monthly payments by about £17 a month over 3years.On the finance calculator it states it's a an Audi deposit contribution so the way I'd see that is that it's not costing the dealer anything. If you've managed to haggle the car price to an agreed value with the dealer then surely the Audi Finance PCP deal should go from there, so their £1000 deposit contribution and APR???
Just make sure it's not the dealer trying to claw back some of the discount they've offered you.