I'm not sure of the exact nature of Apple's manufacturing process when it comes to anodised aluminium, but I too find that substantial scratches take off the top coat to reveal a sort of darker, almost black layer.
My old MacBook Pro (1,1) had a horrible problem where the bottom of the screen bezel (below the iSight) would rub against the casing in front of the trackpad button when the lid was closed... This resulted in the most horrific scuff marks (permanent) where the two sheets of aluminium had been rubbing.
That's the only bad thing about these aluminium bodies, in my opinion. They look and feel great, but they dent and scratch unbelievably easily! 😡