Late reply, but the best justification I have for it is that since the apostles are twins, someone who one infects could potentially develop the powers of both. Ella, for example, is a spawn of The Body, and she doesn't seem to have any access to the memory powers like the MC. During the first evolution you enter some type of dialogue with your monster parent, which changes based on who you chose at the beginning of the game. At this point, I suspect the difference is thematic, but maybe it'll have some more substantial impact. I suspect, though, that the Eye that keeps talking to us will be a more main focus rather than the actual progenitors.
Yeah, that's exactly what I'm getting from the storyline so far. It just kinda bugs me that our progenitor was even a choice when it seems that the Origin (eye thing) is the more important storyline here regardless of how we approached it.
But maybe its a set up for later?
I know thag I personally have two different saves, each with one of the two twins just to see what happens. Lol