I think Sasuke's genjutsu on the Bijuus were temporary, if you look in ch. 699 (I think it is) then you'll see that after Sasuke released CT, Kurama's eyes weren't that of the Rinnegan as they were before which makes me think either the genjutsu didn't last long or when Sasuke took chakra from them, it disrupted their chakra and broke them out. So Naruto using the Bijuus chakra directly from them may break them out in the same fashion.
Also it should be noted that Bee said his power inside Naruto is weakened so I think the same applies for anyone being inside another's subconsciousness. Oh and I doubt Sasukr can even go inside Naruto's subconscious now anyways, remember when Naruto went BM and was talking to the Bijuus and Jinchuurikis? They said Obito couldn't reach that place (Naruto fully became a perfect Jin at that time); Obito had his Sharingan and Rinnegan at the time. This also explains why Sasuke, Obito, and Madara couldn't do this to Naruto or Bee when they fought.