Indeed. I believe it was mentioned on the guide, but I guess it wasn't clear enough and eventually mixed up with the SP/MP thing. Should be corrected by now.
Actually you can even have your modded files outside the AvP folder, just need to set correctly the path of your mod (for eg: C:\PROGRAM FILES\Mods\XXX.en) on the .lst file where you want to apply it and it will work just fine.