Perhaps the Animus doesn't hold two sets of genetic memories--most likely, both characters are based on one historic figure, and the other was made as an alternative character for the sake of player choice. No one adds in an alternative male, so the female is most likely the one made by Abstergo.
As for the dialogue options, those are most likely based on the genetic memories of what the man considered saying, whether he ended up speaking it or not. While adding these in does tarnish the historical accuracy of the simulation, it does add an RPG element to the experience that could attract fans of more traditional video games to the Animus.

SpoilerNow listen, guys? Do you remember Assassin's Creed III: Liberation? As I played through it, a hacker who'd infiltrated the Animus actually helped me uncover memories intentionally hidden away by Abstergo--I'm only gonna say this because Favslist spoiler tags are a secure line: I think Abstergo's hiding something from us. I'm not so sure the Templars really are the heroes--and I don't think Aveline de Grandpré joined them. Keep what I've said to yourselves. Keep an eye out as you explore any games running on the Animus.