As I understand it, you pay the deposit to Ford first then you work with a dealer to finalize the sale. If all dealers are marking them up (they are) then your choice is to lose the deposit or pay a markup.

Edit: Actually it looks like the Ford deposit was $100 and refundable. This must be a separate dealer deposit. I am not sure if it comes before or after price agreement. Dealers are sketchy as hell so could be either.