This must have been the confusingly complex version of Hollywood's "Upside Down". Think of it as a gentle mindf**ker like most Japanese animation is well known for. However you wanna put it though, you still come out of it confused and simply just demanding to see much sense of it all. Despite all that, this story is quite beautifully done.
I hope they make some more and I would love to see a sequel because the story leaves much untold and unexplored as the whole film feels like a first episode of a possible great anime short series for cinema