There seems to be some confusion on how WBFS works... The program takes the GAME partition from the game and puts it on the hard drive. That's it. It doesn't do anything special.
When you take a game off of the hard drive, the WBFS program remakes the ISO file, but it doesn't make it identical to the original. It makes a "scrubbed" type ISO with a single partition (the game partition from the HDD).