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We don't know for sure. The schematics is a "reference design" and may or may not match the actual board. (actually, we know it doesn't match. No map of Italy or Arduino logo on the silkscreen.) One hopes that it matches electrically, but there is no guarantee. If I were the Arduino team, I'd be tempted to include some differences just to help track where clones are coming from.
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Both AVRs need code installed. The 2560 needs a bootloader, and the 16u2 needs usb/serial code.