I think it has to do with Louise has to stay in her world and Siesta wants to go back with Satio to her grandfather's world.
I have a friend from Japan and he translated the news from here!
http://www.jcstaff.co.jp/sho-sai/zer...zero-index.htm
From what was told Noboru Yamaguchi wanted the Novel, anime, and manga to all end in different ways. The Novel would be the Satio/Louise pairing, the anime would be the Satio/Siesta pairing, and the manga has yet to be determined. i guess something similar to how the Shuffle anime and manga ended different ways.