[edit] Might as well relate an anecdote:
When I got my MacBook Pro about 2 years ago I had it built with some custom options (glossy screen and bigger HDD, FYI), which made it a "custom order" in Apple's system. It took a little longer to ship, but anyways.
So over Xmas the MBP bit the dust, and I had to get a replacement from Apple. They offered up a new unibody MacBook Pro, and since the stock model matched the specs on my custom-built one, I was to get a stock, new, MBP.
This was going to take about a week, they told me. I had an Apple Store some 20 minutes away from my home, and I asked if I could just bring in my broken laptop and walk home with a new one. Less hassle for everyone. Nope. According to my support rep, this is allowed if my machine was a standard config to begin with, but their system would not allow a replacement order to be placed if the system was custom!
Rules sometimes suck.
Ideally their script should have an exception or a way to bump to a supervisor who has the ability to make decisions themselves.