I don't understand. Allow me to layout how I thought this worked and someone who is more of a business guru explain (in layman's terms) where I have things wrong.
My understanding:
Apple's retail stores are part of the Apple Corporation, not franchises like a McDonalds (ie. you get the name, but it is owned by an individual or group of individuals who run it). As such, customers (who shop at the Apple Retail stores) are buying directly from the manufacturer as if they had gone to the online apple store. So, the retail stores aren't really buying products from Apple, they are Apple.
Each store (including the online store) has to keep a base "cost" from which to calculate markup and profit. In most cases this "cost" would be the actual cost of manufacturing the product, however I'm guessing Apple has probably added a small amount per unit to pay for running the stores.
Now, by opening more than one store, Apple has complicated things for their accountants. Apple now has to keep track of which stores are earning profit for them and which are losing money. To do this, each store need to keep track of it's earnings and costs (like any store). However, since they Apple store's only expendatures are things like rent, power, etc. and their income is from selling products that Apple has already paid for under a different department. The numbers would be very inflated (every store would look like it was making money).
To solve this problem Apple probably treats it's retails stores (which is a department in the company) as a customer of the manufacuring department. So $$ is transfered between the two departments in the company. This makes the balance sheet (per department) look much better and also allows the company to keep it's eye on which stores people are buying from.
Obviously Apple authorized resellers are going to pay more for a product than the Apple retail stores. Apple has to make some $$ from those sales. Did Apple lie about charging their stores the same as the resellers? I would like to believe that they wouldn't intentionally lie like that, but it looks like they did. Maybe they didn't understand the question and answered as if they were asked if customers were going to pay the same at an Apple store vs. a 3rd party?
Okay that is my $0.02, please let me know where I am off so I can try to understand what the hubub is about.