Freedom Flight is referring to those little ships in the background, IIRC... it mentions the corvette landing and letting out troops, different from the already-landed slave-ships. (So, yeah, you can see them in FF -- but they're no the big round ships).
The cover of End Run is like the cover of Wing Commander 2 -- a carrier that's the same class as the ship in the story, but *not* the same story. (WC2's box has the CVS-14, whereas Concordia is CVS-65... End Run simply has a different Escort Carrier). The fighter is, presumably, a Grakhi.
The theory regarding the woman on the Action Stations cover is that she's the one from the end who's trapped with Kruger (and that the guy is Kruger).
It's possible that the ship on the cover of Freedom Flight is the Kilrathi starbase seen at the end of the book. It's possible that it's one of Fleet Action's Vatari, although I'd rather believe that the SNES SM1 heavy fighter thing is a Vatari, since it better fits the description.
Don't think there's anything wrong with having an Excalibur in different colors -- although Excaliburs are only vaugely mentioned in False Colors.