With the God Tree fruit in Naruto, I decided to link the two manga just for fun. I'm not serious with this theory, like I said I just made it for fun.
Please read Naruto Chapter 646 before continuing.
Let's say that the God Tree successfully absorbed all the ninja's chakras including Naruto, Hashirama, Obito and Madara. But knowing Naruto, he will not give up that easily even there's no chance of winning. With Hashirama on his side, Hashirama told Naruto that they can seal the God Tree using their remaining Sage power. The God Tree on the other hand is busy absorbing all the chakras in the world so that no one can ever use it again. Hashirama sees it as an opportunity so they decided to give their all into that Sage sealing technique and sealed the God Tree forever. But even though they sealed the God Tree, their chakras will never come back again because the God Tree successfully absorbed all the chakras in the world.
After the chakra vanished in the world, the only thing that can harness is sage power or natural energy but without chakra they called it Haki.
After the God Tree incident, a phenomenon occurs. They found fruits that grants amazing powers. They believe that it came from the God Tree and because it is cursed, they call it the Devil Fruit.
At chapter 646 Madara said "the flow of time gradually erased people's memories about how things were in the beginning".
The God Tree incident and the chakras happened in Void Century which is inscribed in the Poneglyphs.
This Poneglyphs is the same with Uchiha's stone tablet of secrets that can only be deciphered with Mangekyou Sharingan and Rinnegan. Even though the Sharingan does not exist anymore (It got absorbed along with the chakras), they found a way to create the same tablet without the use of eye techniques which is invented by the Uchiha.
Now the place where Hashirama and Naruto sealed the God Tree is known as Ohara island (Nico Robin's origin) were the Tree of Knowledge is located. This Tree of Knowledge is said to be as the living form of the God Tree and the people living in the island are the descendants of the Uchiha so they have the ability to read the Poneglyphs.
Chakra = Devil Fruit
Sage power = Haki
Uchiha tablets = Poneglyphs
God tree = Tree of Knowledge
During the fight between Naruto and Obito, Naruto can only hurt Obito with use of Senjutsu / Sage techniques like Haki vs Devil Fruit.
It is natural that Haki can defeat Devil fruit users because Haki is derived from Sage powers and Devil fruit from Chakra powers.
Thanks for reading!