Cinderella's Prince is a Time Lord.Hear me out. The Wolf and Cinderella's Prince are often played by the same actor. This is because they are in fact the same person. We meet The Wolf, who is killed before we meet the Cinderella's Prince. They are both very womanizing and, most importantly, have repeated lyrics. "...so many worth exploring / Just one would be so boring." How else would they both have known those words? Everyone thought the Wolf had been killed, but instead he regenerated when no one was looking. He then returned to the castle and attend the festival. Due to a freak accident his mouth is the door to his TARDIS, which is how he fit two whole people, totally alive, in his belly.
The Witch didn't die.She simply placed the curse upon herself again, her beauty gone but her powers restored. All that smoke? The curse taking effect. She then promptly magicked herself away. "Give me claws and a hunch, just get me away from this bunch."
The Witch and the Baker's Father had a fling.It was brief and lasted while the Baker's Mother was pregnant; the Baker's Father had fallen out of love with his wife and liked the Witch's exoticness. The Witch went along with it for a lark until the beans were stolen. Besides, just listen to the dialogue between the Witch and The Mysterious Man - don't they sound like a pair of warring exes? Also, it's nice irony against the Baker, whose Wife (briefly) fell out of love with him.
Jack's dad isn't dead.He left his family when Jack was very small to seek his fortune, and is now the hero of another fairytale somewhere far away— probably, given the world they live in, a fairytale that involves realising how callous it was to leave his wife and child for twenty years without sending back word, and discovering that he can't find his way back. Somehow, this (or a vaguer version of it, anyhow) is how Jack's Mother's line "Your mother's getting older, your father's not back" always read to me as a kid— at least in the American Playhouse taped version, her delivery sounds more like resignation to the fact that he's not returning than that he's dead but she doesn't want to tell Jack.
If the Narrator had lived, the Giantess would have forgiven Jack after he turned himself over to her.The Narrator wanted to tell a story with a moral about facing responsibility and reconciliation, something that would take a little nudging from him and wouldn't easily be possible in "real life". However, killing him meant no one could direct the story toward a theme or moral like he could do, albeit just one about life's unpredictability and harshness. Some elements, like the Baker's wife learning to stay with her family after her fling with the Prince continued as planned after his death, but it too was messed up by the fact that the Giantess wasn't supposed to be on the rampage then, hence killing her.
Little Red Riding Hood's Grandmother was a hunter.She taught Little Red how to skin a wolf, and not everyone knows how to properly skin an animal. And she gave Red a little hunting knife for protection. Also, the way she asked the baker "What kind of hunter are you?" sounded like she was really saying "You're a disgrace to us all!"
The Witch turned into dust.When the beans are misplaced, she does turn back to an old crone. However, she ages so much she turns into dust. This would be because she lost the beans twice, so it is a final punishment.
Jack's father is the Mysterious Man OR the Mysterious Man and Jack's Mom had an affair.In the script, the two never meet. The closest we get is the end of Act I, when Jack's mom runs in yelling about the dead giant. The stage directions say:
The Witch was only twelve or thirteen when she placed a curse on the Baker's parents and stole RapunzelThis would just explain so much about her parenting of Rapunzel - she got the child when she was too young to know how to take care of one. That's why she does so much to be the perfect parent and her love of Rapunzel is expressed in bizarre ways. She wants to be the perfect mother for Rapunzel, but the only way she knows how is to lock her up and provide everything for her.