Possibly through the character creator program?

I'd love something like that, it'd save me the time of having to pull out the geck and modify their stats/appearance manually.

There are mods for FO3 that swap out NPC models at run-time, so I'm fairly certain it's possible or will be possible with NVSE. I certainly hope so, since I'm planning to do this in the mod I'm working on

There's a new script command which might prove useful for that, SwapTextureOnRef.