As far as I know, there are only a handful of private servers out there. I don't really allow discussion about them here, especially the ones that don't use the files we have available here. But for the sake of the technical curiousity presented in this question, I'll allow it.
I can only give you a guess, but there are couple options available when you don't have the source code.
Patching the game binary to change location of the libconfig.
+Modify the file format, maybe to xml.
+Moving it to system settings/config folders for the game.
The most simple explanation would be that they change the file status to hidden. lol
Anyways I don't know why people do these things, nothing short of encryption would even slow down a serious reverser. You only help your enemy if you underestimate them.