Using the G6S tranny of facelifted E53 will mean you have to manufacture the rear shaft, which is going into (pre-facelifted) NV125 transfer case. Other way, you have to swap the TC too, which is electronically a bit complicated, but doable. IMO, the pre facelifted TC (NV125) is a better choice, due to it's simplicity and reliability.

On the other hand, going that far, you can also use the GS6 tranny, NV125 transfer case and LSX engine - the effort wouldn't be much higher indeed.