I had heard that products sell for the same price everywhere in Japan, so how can prices and the rules for returns be so different at different stores?

In Japan, stores can set whatever retail price they want. For that reason, at different shops you will find different prices even for the same product. Also, in Japan, as a rule, you cannot return an item that you bought at a store simply for personal reasons. The store may have its own policy on returns, in which case you might be allowed to return the item.