It doesn't matter. It's all become a part of them through breeding and it's been shown over and over that when chakra is extinguished, the bearer dies, or did you not see the shinobi shriveling up and dying when the Shinju sucked out all their chakra?Nobody had charka until kaguya stole the fruit.
Its a Shounen manga, they always end with the hero being OP, this really shouldn't be a shock.They are overpowered.