Class skill cooldown is also affected by the mod which is supposed to be only for fairy skills. The reason why you are not supposed to turn on auto battle and play it manually and use only the fairy skills when the mod is enabled. The cool down of class skills are visual only except the fairy skills.
Im playing with it by allowing the mod menu open all the time, so if all my class skills are in cooldown, i can enable the fairy skill cooldown mod and then spam the fairy skills. I will disable the mod again if i think all my class skills are available again and turn on auto battle or just press them manually. You just have to learn how to play with it.
