It's still pretty easy to fit in Nate as a grandfather even without altering reality.
Kuasa knows who her grandfather is and it's not Nate. Doesn't mean she's right.
For all we know Amaya becomes pregnant finds the "grandfather" of Kuasa and Mari and marries him. Of course that still raises the iffyness of making Mari being partially white, even if the show doesn't completely seem like it cares about that.
But I've assumed ever since Amaya's role grew in the show that SOMETHING would be changed subtly or otherwise to have everything still on track.