There seems to be a conflict or something among the NPC costume mods in the compiled mods section (using the installer). If I select "most females in STO naked" only by itself, almost all female NPC's (minus a few random tellerites and such) will be naked, including named/quest NPCs and bridge staff.
However, if I also use the custom choices options to turn male random NPCs into females, only the randomly generated NPC's will be naked. Named/quest PCs and non-BOF bridge staff will still be fully clothed (excepting clothing items modded by the main clothing mods). The options to change the female NPC clothing into one of the nude-modded clothing sets doesn't seem to apply to named or quest NPCs.
Currently I can't seem to have both nude named/quest NPC's and all-female random NPCs at the same time.