Might be stating the obvious here but,
If you want to work out the finance on a discounted price, then simply pop in the amount of discount in the deposit section (on top of your own deposit). I did this and the quote form the dealer on order day was within pennies of the online calculator.
What is a bigger issue with the online calculator is the length of time it takes to get the car. The quote you get on order day is only valid for a certain period (30 or 90 days?), which will pretty much be way less than the actual delivery time. Very strange way to run a business though, enticing customers in with attractive finance offers, only for them not to be valid at the point the car is delivered !