I'd say they're lying. A dealership can special order anything, with any specific packages. It just takes 4 or more months to get it. They have even more package options to choose from than what is posted on www.lexus.com. Most of the options are scaled down versions of the website options.
They pay the same invoice cost (with respect to added options) than they would getting the car in a normal yearly shipment. That means they have the same price wiggle room (MSRP - invoice). It sounds like they are lazy and don't want the hassle.
I would deffinately not deal with these jokers. Talk to other dealerships, even if they are a couple hours away it's worth it. One warning though, if you do special order, do not expect to be told an exact date for delivery. They have an absolutely terrible tracking system. They do not know the car's location or the expected delivery date, even after it has been loaded on a truck.