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Ok, so the larger components are in the same basic locations, but as you said there are only so many places to put anything. Apple must have spent a lot of time discovering where is the best place for the components to make the Air as thin as possible. Chances are pretty good that these are then the ONLY way they will all fit together for such a thin tablet.

Looking in more detail at the mainboard, there are vast differences on a smaller scale.

To call the Zen a "clone" of an Air would be like saying a Ford is a clone of a Toyota because the engine is in front and the wheels are at the corners.