That has no bearing on the fact that the Genjutsu was already cast, and that Bee broke out of it. That warning only applied to future Genjutsu attempts, not one that had already occurred.
And Naruto fully understands the machinations of Tsukuyomi, of course, despite having never been cast in it nor possesses a Sharingan.
Fact of the matter is that any Genjutsu requires you to overwhelm the opponent's illusory defenses, and the only reason it worked so easily was because Part 1 Kakashi and a 5 year old Sasuke had pathetic illusory defenses compared to Itachi.
Hebi Sasuke showed that Itachi cannot simply Tsukuyomi a competent target and call it a day; he has to overwhelm the opposition's defenses, and will be rendered immobile, unable to capitalize on any openings until said illusory defenses have been defeated. The same is shown with Kakashi vs. Obito, where neither fighter moved until the Genjutsu was over.
