I would argue it is just the writer wanting to give a happy ending.
I dont believe the real Emet-Selch would just quit and abandon his objective of bringing back the original and whole and better civilization because one out of the 14 parodies of existence did something cool once, the way he acts at the end just felt of but that is the issue with such antagonists, you cant satisfy everyone, only one person wins, one loses, so trying to make a situation where everyone wins is just kinda wishful writing.
I can absolutely understand seeing the WoL as someone who MIGHT have a chance in this new world and somewhat respecting them but not that he would accept that the entire ORIGINAL civilization is now dead and gone, especially when it is absolutely possible to still bring it back via the rejoinings.
Honestly I felt we would have achieved better results if we joined him back in shadowbringers, even made a
thread discussing that very topic.