Piro discusses Circuity in his rant column below this strip.
It seems like I'm missing something because I haven't seen Haibane Renmei.

Piro speaks:
(sigh) you know, this IS the equivilant of a Haibane Renmei doujinshi. You know, doujinshi? those works that thousands of japanese fans do where they set a story in the world of some anime they love?
That doesnt mean that i am insisting that you go and see HR. You dont have to, i tried to keep things as ambigious as possible so you would be able to understand it one way if you are a HR fan, another if you arent.
you don't HAVE to understand EVERYTHING you know. I never could understand that NEED most people have, to completely understand things before they will allow themselves to enjoy it.
lighten up, enjoy the ride, or decide you don't want to ride it. Its not like the characters you are traveling with understand everything that is happening to them either. Maybe readers tend to have some sort of god complex or something.
Hell, even as the writer and creator, even i'm not the "god" in these stories, believe it or not.