This is not because Apple wants to shaft you but simply because Apple may not have that model for sale in their systems.
If Apple doesn't have this model in question for sale, there are other issues. This is a brand new iMac. Also Apple has exchanged other computers for better models when an issue occurred. So, your statement can be marked as invalid.
Amazon may custom order models, sell older models, order models without RAM to use their cheaper RAM (as is common with MacMall), have specific "Amazon" part numbers, etc.
Try again. How many Apple custom configs have you seen on Amazon. Amazon even shows the Apple part number, so there's nothing fishy going on there.
As such Apple will can only repair the computer. Again, would you call Samsung and expect them to ship you a new TV or would you go back to Best Buy? I know hands down, I'd be back at Best Buy.
But Best Buy offers support, whereas Amazon does not. That's the difference between a VAR and a reseller.