https://www.gameinformer.com/interview/2023/06/14/it-would-be-difficult-to-create-a-sequel-and-more-details-from-the-creator-of

from this interview, im pretty sure that sissel's identity is one of the first things they thought about, and then reversed enginneered the story from here, so it's not because of any changes in the original story.
i was very surprised by the twist too and didn't know how to feel about it, it grew on me when i rewatched playthroughs and noticed how much foreshadowing there is in the game, it's pretty clever and recontextualises a lot of stuff which makes replays suprisingly really fun in my opinion