I am not sure whether this is a bug or a feature, so I'm putting it in GD&F rather than elsewhere, but special officers (like the Android BOFFs) seem to be tied to the Federation (2410) faction when bought at the TOS (2270) version of ESD. When you then attempt to commission the BOFF, you're told their allegiance is to the Federation, look to your own empire.
This could well be a feature, since Soong-type androids weren't around at that point in time, but if so they need to be removed from the TOS store (along with a load of other TNG-era items such as Bajoran foods in the bartender vendor).
It could also be one of those "still being worked on" things, in which case, cool, looking forward to seeing the result.
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if you look at available ships all you have is the pioneer and connie. you can not use the NX, or oberth