I fully understand why you would specify a gloss finish for durability and matt finish , as nice as it might look, won't prove as durable.
This car is alot of money and it needs to be what you want or you'll not be satisified with it. It would always be a case of "if only" - after-all its not a case of changing a few decals is it.
I'm no paint expert but putting a clear coat over the top might not work. The normal metallic silver is a base coat with clear over top. the matt finish stuff isn't a base-coat as i understand it.
Don't be bullied or inpatient to get into your car. If they need to build another as per your order and you need to wait so be it. perhaps Mr M.R could lend you his loan car by way of re-dress while you wait?
Don't be fobbed off - its your money that i guess you had to work hard for.