It does mention "It is written that a pure hearted warrior will claim the power of the Lords of Shadow as his own." If this isn't apart of IGA storyline it will mention it because Mathias in his own right was a pure hearted warrior (not a fighter but he did participate in the Crusades) and he did claim the power of darkness as his own. So far Im getting the feeling that this story will be a departure and make a new storyline strong enough to stand on its own. So I guess in a sense it would be a side story.
You make an excellent point. While I realize that the development team may not be directly copying any aspect of the pre-existing Castlevania games, but look at Gabriel. I'm thinking that he does resemble a younger version of the CotM Dracula. Still, Gabriel's wife died at the hands of a monster, obviously, not humans. As such, it's still a little hard to believe that Gabriel holds any sort of grudge against humanity and eventually becomes Dracula.
I'm expecting more of an Anakin Skywalker approach, in which Gabriel submits to the "Dark Side" in order to save the one he loves, still ultimately losing her.