Sure something in the store will have a double markup, but what about the items with only a couple of dollars in markup. We had electronics stuff with 50% markup, and we had loss leaders with nothing to get you in the door. Individual items don't mean anything, thats the bottom line. Selling a demo model/returned item cuts into profit, theft cuts into profit, etc.
At the end of the day, things don't look so grand. Sure they'd all like to only sell 50 point gp items, but it won't happen.