If you buy from Best Buy or Apple you get a $100 gift card. If that doesn't matter to you, then I'd purchase from Mac Mall because taxes will run you from $70-$100 anyway and they are tax free in many states.
You still get the 1 year Apple warranty and you can still purchase Apple Care. The Apple Geniuses won't care where you bought your Mac as long as it is still under warranty, and honestly I'm not even sure if there's a way for them to figure out where you bought it.
Anyone else notice that the 4GB of RAM on the 13" MBAs are listed at 1066MHz DDR3 RAM instead of the 1333MHz listed on Apple's website? Also, the model numbers are different, too. MC969LL/A on Macmall versus MC966LL/A on Apple's website.