We've been told the whole armies were coming for *chapters* now, it was said that they were close and converging and it was a matter of time until they got there, and the baddies managed to summon the junbi without even needing to kill naruto, so why would they even *bother* genjutsuing him and not killing or draining him straight away. Also there were zero markers that this was an illusion either in-story or meta, and this manga is not subtle with the mindfucks. The genjutsu theory is kinda stupid, sorry. :/

The spinoffs don't ping me much, sadly enough. :(