I don't really understand, so that was Sanae's mom and she left Sanae with Suwako and Kanako? So this doujin takes place in the outside world and later they move to Gensokyo?
This is how I understood it. It is Sanae's mom and little Sanae. After she left the shrine, her bf/lover left her after Sanae was born, so she moved back. Partly because she was sick (I think). She wanted to leave Sanae with someone she could trust. It's subtle but she says Sanae "is stronger" than she is.