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Yeah, Khan has to pay the penalty. (I don't remember GenKhan's card off the top of my head, but Reliant Khan pays his penalty making him 6, but then all upgrades he has on his ship are normal cost.)
I'll have to try it out sometime. I'm a Dominion only player, but I do have back-up Klingon and Federation fleets. Wanted to see if some of my other guys could use the Independent stuff efficiently. It may still be worth it in the end even with the penalty.
11. When designating a non-Independent ship as an Independent Flagship, does the ship now possess both Factions? If so, does this remove Faction penalties for Independent cards placed on that ship?
Yes and yes. For initiative purposes, use the ship's original printed Faction. Using an Independent Flagship also allows the use of Independent cards on a non-Independent Ship when using the United Force Admiral's Order.