hmm don't really understand it since i haven't seen madoka. i still can't bring myself to watch it cuz it looks very depressing. even this doujin made me sad but still a good read.
I suggest you watch Madoka, it's a good anime and it's not that long either. You would understand better if you watched the show. Yes it's depressing but just watch a funny anime right after you finish it and it will lift your spirits!