I'm surprised that so many did not make the connection between how your parents died and the presidio companion. I mean, that companion was on your parents' crew. And mentions how they died. What, you think they made five different conversations for each and every one of these companions depending?
And, as far as I know, it is the only difference that choice makes in the game. I'm sure it will come into play later, when we get to El Dorado, but not yet.