I believe the SE should have come standard with the side moldings. The XE doesn't have it by default, but many were on dealer lots with the side moldings and the buyers were charged for it. It sounds like they are trying to fuck you buy giving you an XE at SE prices. Does it have a factory sunroof? That is the big difference.
By the way, I thought the strips were sold as a set of four, but it was still around $200. I had a door reskinned on mine and the bill had the charge for one replaced as the price of a complete set. You also might try
http://www.xterraparts.com