>>16865Muetta is a cloning, but Yukina could just be a distant relative of Yukihime. Both her mother and sister have the same hair colour. That doesn't actually explain "same generic code," but then again, anime. I don't really think this anime will go heavy on the twists.
If anything does get revealed it is that there could be more than one Yukihime clone send through different time periods. Don't forget the legend of Kaguyahime. Sure it is a different name, but it seems relative enough. I see no reason to believe the original Yukihime wasn't send there, fell in love with humanity and protecting it. There was even the thing where she meshed her own blood with Ken's blood to activate the mech, otherwise he shouldn't have been able to do it. The weird thing is they don't seem to have any way to control or even find Muetta's positions so I a don't see how they can use the clones as infiltrators. If Yukina gets mind controller without even using their bug it would be a big asspull, though there is also a chance that they are cloning their own mythical princess and she is connected to the stones. But again, I find all of this being too much for this anime, but Japanese are good at making unnecessarily forceful endings.