They don't need Sega's permission to replicate the Genesis, the patent ran out this year like it did with the Famicom in 2003 and NES in 2005. They only need permission for the games, which Sega seems to have a pretty steady approach to letting 3rd parties use them. Nintendo would never let them pack games in with clones of their systems, even if it were licensed.
Nintendo really doesn't care about cloned systems since they appeal to such a small market in North America that it doesn't matter. SNES clones are technically illegal until 2011, but no one has been punished over the FC Twin/Retro Duo.
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