Nice story. Not certain that it will make a favorites list, but it made my morning commute better.
To answer some of the questions lingering here, my listening of the story indicated that the free will and memories started with the drop of blood. Blood magic is a strong theme and powerful agent with homunculus stories. It also tends to lead to unintended consequences when the blood is provided by someone with passion or in a moment of passion, as it becomes a literary mechanism to transmit emotions and passion. With the drop of blood, the perspective altered slightly.
The fingers disappearing coordinated with different feathers being plucked - crow, swan, peacock, and pelican. The fifth one, the thumb, was the phoenix. After being reborn while a phoenix, the homunculus regained his four previously lost fingers. This would fuel his logic in that turning into a phoenix would heal the child.
Something that makes the story all the more tragic is the suffering that will continue after the story is over. A child in thin clothing in the woods two days from town in the winter doesn't have great odds of survival. Also, there's room to turn around the alchemist as a character. Yes, children died before during failed experiments, but he fixed the flaws and the experiment works with the subject surviving the ordeal. While the child was the victim of neglect and abuse, an argument can be made that it was the only method the alchemist could devise to keep the child weak and therefore controllable during the painful experiment. He only needed a phoenix feather, not phoenix blood, so the girl would have been alive and whole at the end of the process with or without the escape. I'm not sure the escape was a good thing. The alchemist will likely be killed by the prince for failure to produce a feather. The child will die in the snow due to exposure. The homunculus will have his shiny eyes pecked out by birds, and wander blindly as he slowly falls apart. What a horrible tragic story.