To be honest, the companions never really reacted or interacted with Lana or Theron, when any cutscene played they were just there, but it was as if they weren't really there, they were just standing a bit further off not really doing anything, just standing there. I think they were just playing the part of the players in-game companion, but for the actual story itself, they were never really involved until after KOTFE & KOTET when they came back. So, this is more a Story Vs Gameplay scenario more than a plot-hole of sorts.

That armour set is a unique version of the Callous Conqueror set, and only those 2 characters have it. I could definitely see him secretly pretending to be some lowly lord acting as a sort of liaison to the alliance and likely reporting back to the rest of the Dark Council (Or keeping the info for himself for his own power plays).

From what I saw in the PTS, there will be complexions that can be used to add stubble, seemingly it works on all humanoids, including Miraluka and even Chiss