Im going to have to say no only because it seems very rushed and forced, im sure he had the idea of the origin of chakra in his head since forever but not specifically the character of kaguya.
No you damn baboon. Its obvious he writes the story as he goes along. The only thing he has had planned is the ending Sasuke vs Naruto fight and thats not changing.
it doesn't really seem that way at all. the sage himself would've been fine as the origin of chakra, or rather being the first to teach how to manipulate it. To me it just seems like kishi is trying to link the three great dojutsu together and throwing the bone KKG in there for who knows why