The characters are split out into 3 latyers. Base, which is the body and head, the Hair and then the Tools/Hand. So yep, you change the skin tone in the tools_ and base_ layers sprites and then the hair separately. The intention is that you'd use palette swapping to change the colour of the hair and skin via code so you can have endless versions while only using one set of sprites. You could also just recolour them by hand but that'd result in a lot of sprites! This asset was quite useful for palete swapping years ago: https://pixelatedpope.itch.io/retro-palette-swapper