That's Kishi's job for reasoning.
I predicted this just because Shisui erasing his existence even after giving his eyes wasn't acceptable for me.
Also Sasuke's and Naruto's dream clashes but there won't be an eye-for-an-eye battle between those two. There should be a strong reason for their battle. Kishi's reasoning for Shisui's return might lead to this way. After all Sasuke accepts whatever said to him. like he changed by Obito's words then Hashirama's words.
Anything is possible with this manga.Btw nice theory with some solid proof mate.I won't mind seeing Shisui as the next villain if Kishi decides to continue.