[@Krot] He can see even if fully smoked, right? That's enough for vision based. As long as you SEE vision based ones, it affects your chakra flow anyway. If he cannot then well, obviously vision based doesn't work.

I'm unsure if he can smell or taste in that form, if he can, then they work too. 

If you mean APPLYING a genjutsu can't be done when he's in smoke mode, that makes more sense, rather than purge genjutsu he's already succumbed to for free while being immune to future applications. 

Thing is, I don't know how a cloud of smoke is supposed to feel and what senses it has. Only OBVIOUS immunity is touch based ones. 

EDIT: Vuur i am the genjustu minister here pls, call me tuuj 2

EDIT II: All genjutsu are sensory based. I have one that directly affects chakra instead of senses, but otherwise they are all applied via a sense. Infinite Tsukuyomi is barely even a genjutsu.