I think there's some confusion here -- "Apple Authorized Reseller" does not mean "Apple Store". B&H is authorized, Amazon is authorized, Walmart, Target, Best Buy, and T-Mobile are authorized resellers. There's a tiny local shop near me that's authorized.
There are only ~500 Apple stores in the world. There are probably probably 100,000 authorized reseller locations (Walmart alone has 10,000 locations).
Setting aside Apple, the reason companies set up authorized reseller programs is to control the customer experience, from price maintenance (the topic of this HN thread) to brand image to customer satisfaction with returns/refunds.
Being authorized for any manufacturer is kind of a big deal; these companies pay for that arrangement, and there are often training requirements for staff, and minimum purchasing requirements, requirements for return/refund policies, and more. In return, the manufacturer steers business to these retailers and provides them with (often free) brand collateral, demo units, etc.
So if a customer has a complaint, whether it's user error or defective product or a mistake by the retailer or just the customer deciding this product is not for them, there is a strong incentive for the retailer to do right by the customer to avoid jeopardizing their status as authorized.
But if a customer needs help from a no-name reseller who has no direct manufacturer relationship, that reseller has little incentive to fix the issue. It's cheaper to just punt everything to the manufacturer, and there is no reason to do any extra work to protect the manufacturer's brand.
And of course unauthorized resellers have a strong incentive to pass off refurbished or even counterfeit products as real. Lower cost, and there's no bridge to burn with the manufacturer.
So all of that is why I think it's plausible that Apple, and other manufacturers, see increased costs and more negative brand experiences from companies that don't participate in their authorized reseller programs. I'm sure there are great indie companies that do everything right. But, in aggregate, at the scale of an Amazon.com, it seems reasonable for both Amazon and Apple to use the authorized reseller designation as a filter for sellers more likely to treat the customer well.