I thought it would be mutually beneficial.
From a practical standpoint, yes it would make sense.
Unfortunately, inventory control isn't handled by practical, all knowing people that blindly trust everyone is working for the greater good. In fact in many cases, the process isn't controlled by people at all. But then, this has a lot to do with the fact that a lot of people
would scam the system if they could.
There's a reason why every MacBook Pro box has a a series of barcodes on the side of each box that match up with serial number on the machine inside. Not everyone has the pure, practical, good-natured intentions that (we assume) you have. Others have been known to do this exact same thing for the purposes of scamming Apple and Amazon. If this inventory process check were not in place, there
would be people buying i7 MacBook Pros from Amazon, and then returning cheaper i5s they bought somewhere else (or maybe even a busted-up model from last year). To a person who doesn't intimately know Apple's product line, they would look the same on the outside.
Amazon's staff don't read the macrumors forums as part of their jobs. They don't know that you happened to win a $5,000 gift card somewhere else. They don't know that you bought the same exact model and want to return that one to them because you already have yours all nice and set up. And they don't know you, let alone do they know you well enough to believe you're a good guy with good intentions.
All they would see is that you bought an MBP with a certain serial number from them, and what they got back was an MBP with a different serial number. Not being Apple employees and probably not very familiar with Apple's product line, the employee checking in your return probably won't be able to tell for sure that the configuration is exactly the same. They don't know where the new MBP came from, what its history is, where you got it from, or why you're returning it to them instead of the one they sent you. And so, they're not going to accept it.
So, although your proposal WOULD be beneficial to them, the lack of knowledge, the risk, and the fact that most other people doing this same thing
aren't trying to be good little boy scouts means that Amazon isn't going to chance it.