Probably, if they found how to decrypt the system file inside the USB formatted via WiiU, they managed to know what filesystem uses, and, since we can decrypt WUD files, just reproduced it.
Maybe, and this is just theory, they found a file inside the legit game on HDD that nintendo uses like a "license" with the unique keys used for the console, you could, let's say, create the same file and with the wup installer modified, install it to the HDD as if the console made it itself, so the console will recognize it.
IMO, ofc.