Lyric discussion by Mad Ape 

Cover art for The Long Grift lyrics by Hedwig and the Angry Inch

Also remember that in the play Tommy sings something along the lines of "look what you've done, you've made me whole" during the scene where Hedwig is explaining her idea of love.

So the darker version played later (with the above lyrics) is an inversion of the original emotion of the song which helps make the lyrics even more bittersweet.