Apple explained this already. They have high resolution / high speed cameras analyzing each phone as it goes down the assembly line and automatically selecting the 'best' bezel out of something like 64 possible bins.
If you are talking about this: http://www.apple.com/iphone/#video (05'40") then I understand they are picking the best plastic inlays to fit one particular chassis (as the video also shows). But that is unrelated to the outer edge CNC milling.
What I believe has happened there is that the CNC tool adjusts its path to compensate for mounting misalignments by using a feeler. If the feeler is worn out or there's any other issue then the tool may re-adjust wrongly. I'm speculating, but I'm starting to believe it's not a design change; just a little f-up.
the one on the left is much nicer, but seeing as the device has been out for such a short period of time, can we tell which device was actually manufactured first?
Or is this a case of different suppliers having slightly different parts? which seems unlikely for a new Apple product, but the one with the gap between the aluminium and glass seems all kinds of wrong anyway.
Not sure. But I am getting curious about why. It's a hell of a tooling tolerance or it's a Jony Ive last-minute caprice? Considering the overall packaging accuracy I'd be inclined to file it as the latter.