All sorts of things - I do try to indicate this in the "What's going to happen?" section: various temporary files, swap files, sleep images and the like aren't copied, since they have no meaning across a restart and/or will interfere with restoration to a different Mac.
With a "pure" data drive, the sizes will be closer, but even then the Spotlight information may be different (since it's preserved on the destination).
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--Dave Nanian
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