Yeah, I'd look at it more like a bigger dealer is more likely to be able to sell the takeoff AND more likely to be able to absorb the loss if they can't sell it. Unlike some other components that I'd expect a shop of any size to swap out at no charge (or the difference in cost if there is one), cranks don't get replaced very often. Bike shops usually operate on a very narrow margin. Besides looking for a bigger shop that moves more volume, I'd look for a shop that does more custom builds than complete bikes, which a shop like that would also be more likely to do that for you even if it's a smaller shop.

I can't ride anything longer than 165s without hurting my knees either.