After making the below changes to these two configs and creating a new world, I still found the corresponding entities in colors outside of the lists in the config.

{
// The possible sheep colours which the mod chooses from, divided by a comma.
"possibleSheepColours": "black,brown,gray,light_gray,white"
}

{
// The possible shulker colours which the mod chooses from, divided by a comma.
"possibleShulkerColours": "normal,black,blue,cyan,gray,light_blue,light_gray,magenta,pink,purple"
}

Apologies it took so long for me to get to this. I have it confirmed working, but it does require a restart of the game. I think that might've been the issue. I'll add it to the description on the mod pages to avoid confusion for other users. Thanks for giving the mod a try!