If I recall correctly, in typical paranormal/religious lore, the title/setting makes sense, as, usually, the ones that tend to end up in Limbo the most are usually children like the Boy and his Sister.
In the ending the boy approaches his sister, who is picking flowers by a rope ladder to some treehouse. The title screen is that same area, only the rope ladder is broken and flies are hovering over what appears to be dead bodies. Theirs?
Is she picking flowers, or crying? Why is she crying?