pkNX edits a folder that contains a ROM dump. Any files that are changed from the ROM dump are stored in the ROM dump's folder, inside a 16-digit folder (ROM's Title ID). This Title ID folder is what you copy to your console, and the console's layeredfs feature will load the files from that folder instead of the cart/SD when requested by the game.
When loading files to edit, pkNX checks the Title ID folder to see if the file has been edited. If it exists, it loads it, otherwise, it reads it from the unmodified romfs.
When you wish to revert modifications completely, you go into the Title ID folder and delete the modded files, so that pkNX loads from the unmodified romfs. When the files are deleted, the modded files will be gone, and you should be seeing unmodified data in-game and in the editor.
If you are seeing randomized data in a fresh ROM dump, then you either didn't open the correct ROM dump folder, or you pirated a pre-modded ROM. Neither of which are issues with pkNX. pkNX does not load data that does not exist. It is up to you to ensure you are copying files and managing mods correctly; pkNX is just a program that loads data from where it is told to load from, same as the console.