1) Inner Sakura is forgotten. That thing doesn't exist anymore because it was presented in her younger days.....now that she's older and wiser she doesn't have/need it. So at the end of it all, it's represented as nothing in part 2 and doesn't contribute to anything.
2)Madara's "will" black zetsu was actually Kaguya's black zetsu. Madara was just getting played the whole time until the final act.
3) Regarding the Totsuka blade, it doesn't matter if someone is cut in half or not. If they get even grazed by the sword they get sealed. Plain and simple.
Got nothing to do with even damaging the person.