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Some items might even be at a loss for Costco ($1.99 for pack of 36 water bottles?) but overall I think it's not zero margin enterprise.

Some items or services are definitely carrying healthy profit and behind the scenes kickbacks from the vendor (small business payment systems, other recurring services sold to customers, very large price ticket items like furniture and cars)

This. It's likely deliberate optimization. They want to encourage a larger average order size & higher revenue per customer. You pay for a membership, making you more committed to shopping there. Then they don't optimize the experience to support small orders, so you might as well get a few more things as long as you're there.

Nope, I don't think that's true. At least that's not what they told employees. They told us stores make almost identical money from the margin of most items (I think it was something like almost everything is marked up 20%) and yearly membership fees.