Hi 5Dh. Yes, Taking a deposit or not is up to Dealer discretion.
Not exactly sure what you mean by the Dealer making more money. If you don't take the vehicle, it will be sold as a retail sale to another customer, and the Dealer will not get the X-Plan sale incentive back from Ford, unless the next customer also has an AXZD-Plan PIN.
Unless you mean they would be able to sell it to someone else for more MSRP or more? Eh...I guess it isn't important...lol
Either way, hope you get it quickly and good luck.