Feed stores receive most of their chicks from hatcheries anyway. They are just handling the losses and getting the refunds in lieu of you. They may get more discounted prices since they order in such bulk, however they may mark up the price of the chick where neither option is cheaper. If, however, you prefer a small order of chicks, just 3-10 then the feedstore is cheaper, as you don't have to pay small order charges.
I'd call the feed store because even if they do not normally carry a breed, they may special order it in certain amounts. If the extra's sell fast, they may include them in their lineup. Most feedstores carry a PR, PB, Cornish X, leghorns, and a couple EE's, bantams or something else for looks/uniqueness.
I'd go with the hatchery overall, for selection and price. But if I was doing small orders? Feed store.