From the past and now, using any game mod should always bring our brain with it! Not just open it.
So what you are saying is they are only detecting the amount of skills used? (In short period of time)
Alright, sorry for my bad English which is not my native langauge.
Lets think about the non-modded situation, how many maximum times you can use special move in one quest? just 3 right? and how many purple ball you can get in one quest? ans. is 1.
At the beginning of the normal quest, your character coming with 1 special move quota and get one purple ball before moving to the boss area. So there are two special moves you can use normally. Thats the major point of the detection.
And the normal skill part is the other possible detection, one character minimum skill cold down time is equal to original cold down time minus sub-character de-cold down skill. Thats another maximum detection point!
Hope you get what I mean.