I can only answer you from the perspective of what I know about modchips. The modchip is there to stop the boot process at the right point to allow a backup to be swapped in. At that point, the region and disk authenticity checks have been made and any PS2 game that has been correctly copied can be swapped in behind it. On that basis, what you want to do ought to work since the trick you use amounts to the same thing. Try it with a backup of a non-protected game made with CloneCD otherwise if it doesn't work you'll be scratching your head due to additional complexity. Let us know what happens.