The turning back time for Dios is also explained/hinted at in the little footnote that says something similar to:
"In contrast to what most people think, pyramids do not make razors sharp, they just take them back to the time before they were blunt..."

So, when Dios goes to the first Pyramid, he goes to have time turned back for him. (To keep on serving the Kingdom)

As for the ending of the book, reread Khuft's dreamtalk with Teppic. Then read the end again.