[Souten no Seigyoku]

I think they're already under the genjitsu. Since he was fighting Madara, he was "in the eye of the storm" so to speak and has fallen under it before the others.

The supposed idea of the genjitsu is that reality goes away and you live in your own dream world yes? So Madara would be with Rin living his dream life, etc, etc, but Naruto's shtick is to never give up. So he'd probably still be fighting Madara. Sure his dream is to be Hokage, but he would notice he was fighting Madara moments ago.

Technically he doesn't have full control of the Kyuubi because his dad has 1/2 of it, so the Kyuubi couldn't wake him from any genjitsu like Bees Biiju can. Plus it' no ordinary gensjitsu anyway.