Doesn't this (except for the counterfeits) apply to Costco too? Is the difference just that Costco never pretended to be an open marketplace, just like how Apple never pretended that iOS is an open system?

No. When you go into a Costco, Costco is a retailer who bought merchandise to sell to you. When you go to Amazon, a large amount of the products are being sold by third party vendors while Amazon is taking a large cut.