We've custom ordered 3 cars over the years. It's a good way to get what you actually want in a car, instead of how the cars come optioned as ordered by the dealer - or just packaged with popular options by the factory -"sales bank" cars. Generally you need to wait a couple months for delivery, as the car is built to your specs.
So maybe you want a car in a Certain Color , with certain go-fast performance options, but None of the navigation / entertainment / luxury seating / power everything / distance control garbage. Most likely will not find your desired set-up on any car lot.
So a person could buy a vehicle they have on the lot, with extraneous, heavy do-dads, 2nd choice color etc -- and compromise your wishes+ pay a generally higher price point -- or leave a down payment and wait for it to be built + delivered.
Both of the major manufacturer vehicles we put about $2000 down, had researched prices beforehand [ Edmunds, etc] , and paid $500 over actual invoice cost [ because edmunds spells out invoice cost of each option as well .]
Also , on sales bank cars, the 100 or more vehicles the dealer has sitting on the lot for someone who needs a car Today, the dealer generally has a "holdback" cost of several hundred dollars, that they owe the manufacturer for "advancing" them the car to fill up the lot. On an ordered car, there is no "holdback" because the vehicle hasn't been sitting on the lot costing the dealer money as it gathers dust, and taking up space - so the dealer is usually more comfortable negotiating lower on price.
Nonetheless, kendallf's friend probably should have just given up his deposit, chalked it up to a life lesson/ unfortunate circumstance, and never took delivery of the Mustang. For myself , I'm well aware of the folly of buying a new car vs used, but sometimes dumb choices lead to good screennames....