I think the “why is xyz alive” question could be what the author told the writers. My understanding is he gave them a broad overview of the ending but without joining the dots.
So if he said “Varys pushes Dany off a cliff after she roasts Jon and she goes splat and Littlefinger reveals himself to be the true prince and wins the throne” then those characters are alive for maybe that one moment in the ending so I think from here it’s hard to predict what’s going to happen.
When they had source material they copied it very closely so I doubt they’ll deviate from the authors ending if they have it.
They were quick to dispatch anyone from Highgarden, Dorne, Stannis once they ran out of ideas. I doubt we’ll see the maesters again now either.
So I’m hoping that Littefinger, Varys etc. are here to do something before they die rather than just go down for the sake of it.