In the real world when you buy an aircraft from a manufacturer you negotiate number of seats engine type etc, i know some of this is WIP but something that it may be possible to implement is the negotiation of the price of the aircraft with existing customers of the manufacturer having a greater say. The way it could work is that you suggest a price to the maker for x number of orders and y number of options with specs A,B,C... the value is compared to the base price for this aircraft and then depending on variables such as if you are an existing customer size of your airline etc a price is suggested by the maker for example.
E.G you place a offer of €500(each) for 10 737-400s, this is hugely too little and would upset the manufacturer who would retaliate with €80,000,000(each) which is about €16,000,000 greater than brand new.
If you were to put a more reasonable offer on then they will either accept that value or they might make an offer which is less than the asking price but greater than your offer. The ability to have options may serve some airlines useful as they may find that the aircraft they ordered wasn't as good as they had expected e.g a 747 makes less money on some transatlantic routes when compared to a 767. so if they had options for both they don't need to commit to both types and therefore save time and money to build their routes.