I've noticed that even when I decide to stay neutral in a civil war, my liege is able to raise part of my levies before I do so. Is this WAD, or just an engine limitation?
This is how it works in vanilla CK2. I would just call if basic game mechanic so I doubt the modders intend to change it (if it can be done, and I am also doubt it ; a vassal is always obliged to give levies to its liege when called)
However, I do not see how this defeat the purpose of "mega war system", and I am not even sure I understand what you mean with this.