Ah. I didn't understand the point about the discount on inventory. Thanks for clarifying.
Yes, you'll always have an advantage negotiating for a unit that is in stock.
Another option would be to find the floorplan you want and then call the manufacturer to help you locate a dealer with that model. I would be willing to travel if the price and floorplan were right.
As far as modifying the layout to remove the loft, that seems like a can of worms to me. I wouldn't do it. Don't give the manufacturer a reason to void your warranty.