"Naruto" is the name of the protagonist in Jiraiya's book. The book is called "The Legend of the Bone Ninja". Jiraiya came up with the idea while eating ramen. After reading the book, the fourth generation hoped that Naruto could become a ninja like "Naruto" in the book, so he decided to use this name, and Naruto's mother also agreed. Therefore, there is no contradiction between the two.
By the way, "The Legend of the Bone Ninja" was written when Jiraiya was taking care of Nagato and the others. The inspiration for writing the book came from Nagato, and the name was inspired by the fish in the ramen. plate.
You can also understand that the fourth generation quoted the name of the protagonist in Jiraiya's novel.