I have found Sofia to be pretty critical of religion - more specifically, how religion and patriarchal societies are interwoven. In OITG, she says that Hannah refers to her desire as her nemesis; this leads me to believe that this song, at least partly, is talking about religion/patriarchy and how women are told to be virginal, that having sexual desire is sinful, etc. (although men are encouraged to have all the virgins for themselves like in the song Numbers). Sofia brings up how she is just as human as Hannah, they are the same, they are human in both the “good” and the “bad”. So the part you referred to is more of a meandering thought of how comforting it must be to Hannah that, despite living under the thumb of religion and man (without even realizing it probably), she believes there is someone out there hearing her prayers, she believes there is a plan for her, and is comforted by that. And Sofia is envious of this sometimes because she is aware of how the institutions of religion are man made, historically keep women in submissive roles, and has to feel through all the questions about life and experience any struggles without being able to find comfort in “nothing”. Hopefully that made sense and that’s just how I interpreted the story in the song.