I also realized after a few hours that I'm used to Ren'Py and forgot your game is in Twine, so I don't know if there is a LayeredImage equivalent for Twine.
I'm sorry to hear it's not an option for you right now. It would make things easier in the long run. Adding more layers for my characters and recoloring within the code rather than several differently colored files of the same image in my own game has made customizability so much easier and the overall file size much smaller.
I'm enjoying the game! Just started playing yesterday, but as an artist and game-dev-in-progress the idea of every possibility being drawn separately, rather than layered, alarmed me a bit haha. I hope things work out in a way that works well for you.