hmmm tbh what i am saying now is not official in any way but my thoughts and other players input to what may have happened after the ending,1.after the ritual it doesnt look like your previous choices matter at that point in the game,2.i dont think you are able to use the rune in the game,but iirc someone further in the comments did point out that after that cut scene with what i presume is a monster of some sort,we can somewhat say that the protective rune plays a part later on in the continuation of the story,3.i am not to sure about the window closing and opening but if the ritual states to do that then ig it might have a role to play.If you want try taking out the flowers instead of placing the flower in the pot in the first scene,it turns out different from the first time :)