I also had finally adjusted to the idea of Doll as standing in for Humanity, and questioning why the Neanderthals were battling each other over the fate of Humanity without ever considering whether or not the Humans would like a say in their own fate. The very last scene winds up with Doll, and by extension the Human race, stealing the show and taking a stand in the battle. In a way, it is a passing of the flag into Human hands. The new(er) last chapter undoes that.
Therefore, my guess is that he wrote this last chapter some time after finishing the book. Perhaps after looking back at it and surmising that he wanted to tie up some more of Finnegan's narrative or perhaps tie it more closely into some of the rest of the Argo cycle.