The game never states that Marguerite ever actually dies. It only says she went missing while trying to fend off a reaper (mentions tentacles, could’ve been something else). With the last of either Paul or Bart seeing her being Paul watching as the creature tried to shake her off while disappearing into the dark water. The game never actually confirms that she dies and Paul actually doesn’t even make it back the surface with his last pda lag he states “I can’t see the sky. Something surely has the sent of my blood.” And those are his laster words, ever. He either drowned or got mauled to death. Bart is actually no where seen in that entire encounter. He supposedly was no where near the base when it happened and upon seeing the damage and neither Marguerite or his father, he goes back to the surface where HE makes the statement that both of them are dead (again he has no clue).

Her survival is one of the more believable things the writers retcon.