It wasn't retconned we misunderstood it. Of you look at the fight it was after Sasuke and Naruto touched Kaguya. She was sealed but it was actually Hogaromo who performed the seal for the Chibaku tensei.
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If you see the rinne sharingan is being sealed off.
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The 2 let go and the seals disappear
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Once the seals reappeared on Hogaromo's hands he uses the seal. It was Hogaromo who sealed Kaguya free the tailed beasts etc.[/SPOILER]
2. Don't remember that it's been a long time since I saw the movie, but regardless the weakest rinnegan user was able to absorb 8 tails cloak in moments. So that's not a big feat for Toneri.
3. I've pretty sure Toneri's TSB's didn't help him against Naruto. Anyway they can just as easily be sucked into a chibaku tensei core and removed from a fight.