He is not really the dark Version of Naruto. The real Menma looks exactly like Naruto and is his
counterpart in the other dimension. The dark-haired Menma is the evil one but I don't know how
Tobi influenced him because he was shown like this ( black hair ) when he first met Tobi
and turned yellow again when he lost against Naruto. We know that he can summon the masked beasts with
a special ritual jutsu so maybe the dark Menma was a fusion between the beats and the yellow-haired Menma.
Also we don't know how long Kushina and Minato were on the mission when they return at the beginning of the movie
in Tsunades office. So their son might have been in the dark mode for a week or more.