I would venture to say that Apple gets a much better deal freight wise when sending multiple machines to say an Apple store, than it does sending one to me via LTL. So in essence, it would be a much better deal for them to exchange it for me in the store, and send it back on a truck that is already delivering to them. I can see that you don't have much freight line experience. That's expected.
The extra labor hours includes me having to deal with an Applecare Rep, then an Applecare Genius, and now I'll have to call an Applecare Rep again to get something scheduled. One extra step and communication that is unnecessary.
They may keep the cash this time, but if this is the standard, I'll buy standard config next time from a 3rd party. Guess Apple won't get the long term direct purchase, as I've made quite a few.
If you Special Order something, say from a store like Home Depot. If the item is defective, you simply return it for a refund. They don't have you take the defective item home, call them the next business day, arrange for a pickup, and then send you another one. There is a reason for that, as its highly inefficient method of servicing the customer and a waste of resources.
Apple just shipped your BTO machine from a factory in southern China to your doorstep in around 3 days. Like you, I'm gonna venture a guess and say that wherever it needs to go, returning that same BTO machine isn't gonna be as simple for your Apple Store as throwing it onto the truck their other deliveries arrive on.
And did Applecare require you to go see an Apple Genius first? That seems unusual, especially since not everyone has an Apple Store within a reasonable distance of their home. If your BTO Mac isn't working, it's not working. You have your 90 days of free phone support, the CSR should have just given you an RMA in the initial call.
And your analogy is awful. BTO != Special Order. Ordering something that a store doesn't normally carry in stock, that's a special order. Ordering something in a non-standard configuration, that's build to order. Companies that do direct-to-customer BTO sales (and I'm pretty sure Home Depot is not one of them) have special procedures in place to process those. I don't know what they are for Apple, but it's presumptuous for you to assume that the system they do have in place must be inefficient or a waste based on absolutely no information.
A simple Google search shows that for Apple resellers that sell BTOs, returns of BTO machines are not processed through the same facility that the reseller deals with for standard product returns. Wouldn't it make sense that the same would apply for Apple Stores? And that maybe, just based on whatever the number of BTO returns Apple estimates they would have to deal with, it's just simpler to have the customer return the product directly?