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So I never noticed this and just looked to see if it was listed in the FAQ, but I thought that the Reliant was both a Federation and Independent ship. But I guess it is only a Federation ship. So when putting Khan on it I'm guessing you have to pay the 1 SP to put him on it but then no 1SP to put upgrades on it.

You got it. 6 points for Khan and then no faction penalty for anything else.