Accessories (floor mats, smoking kits, emergency kits, rear cargo covers) are shipped separate from the cars and can be purchased at the parts counter. These items are not configured with the car. Your car as configured should arrive complete off the truck.
Damage, of course, happens between the factory and the dealer. Most is caught at the processing center at the docks. But if it happens on the truck to the dealership, your dealer has to fix things before delivering the car to you. Parts are not fully available, yet.