The handheld blockzapper, Wand of symmetry and the wrench lets players grief the protections.
I use create 0.3 1.16.3 with forge 1.16.5 with the latest uptade of mohist.

Players are also able to power off/on windmills, etc.

That is pretty normal and common problem with lot of mods, not just Create dude ;) I personally was setting up numerous count of modded servers for people as well as helping maintain them and/or optimize them. There is little to no way to actually make sure other players cannot bypass protection create by other mod/plugin. And also, main part/problem I see is that you are using highly unfinished project "Mohist". You shall try reproduce issue standalone or least with some more basic protection mods like FTB Chunks :D