Re: John Doe senior Enterprise officers in "The Enterprise Incident"
My fanwank is that the officers were slipped aboard by Starfleet Intelligence just for this mission. That's why they're seen and not heard: they're spooks. But they have the ranks to issue orders if the mission goes south, probably to make sure the Enterprise is blown up, and if possible to storm a Romulan ship.
Better than my explanation which is Roddenberry/Freiberger took a couple of dark skinned guys and tossed them in the background to make the show look progressive.
Self-appointed Knight of the Abrams Table! - Thanks Marsden!