This specific example would result in a different answer. Costco does not accept VISA at their stores, but they do accept it on their website. If you were to order an item from the website and return it to the store they would (reportedly) not be able to issue a credit to a VISA account and would give you credit in another form.

At most merchants, however, credit goes to the original form of payment and the credit would offset the original purchase for point/mileage calculations.