Modpack creator decides whether to replace default skins or add on top of them. Still, if you want to see only custom ones you can turn "Allow default npc skins" option off. Skins reverting after finishers is a bug.
Check out readme.txt inside game folder(you can open game folder by clicking the folder icon in Options). Basically, put the modified textures in the right folder, make sure the name is not changed and enable "mod" in game.
Gonna check it out. In the meantime you can try checking if your antivirus is not blocking the game since some people experienced false positives, or run the game as admin.