How doesn't that make sense? Sasuke already shown unable to physically react to A's full speed so Sasuke not being about to react to a Naruto's speed isn't hard to believe. He couldn't react to Kaguya warping him and Kaguya with her Rinnegan and Byakugans couldn't see Naruto slashing her arm.
Naruto fooled Neji, Kaguya, Kakashi, Sasuke, and Obito with his clone feint already. Sasuke, Kaguya, and Obito thought Naruto died by Kaguya and his visual prowess didn't help him any.
It would just cancel the affect on him as Juubito used it to negate Amaterasu that was physically on him.
Naruto is right there so genjutsu on Kurama is broken so now what? Difference between Sasuke and Bee is Bee trained for his power and mastered them while Sasuke is using given powers that he is getting use too in battle but have not mastered.