I wouldn't notch it.
I notched half the frame thickness out of mine, but I have the heavy 8-leaf pack and probably didn't need to.
Also, When my truck is heavily loaded, the bed floor sits on top of the differential housing, and the axle tubes STILL aren't where the frame rail used to be. I've had 1700lbs of sand in the bed. By accident.
I recommend:
Flip the axle, don't notch the frame, ~maybe~ add some ultra-low-profile bumpstops if contact occurs.
I will be adding some tall bumpstops inside my notches, because I believe the box resting (and on bumps hammering) the differential housing is hard on the axle-tube-to-diff-housing connection. It may even bend the tubes? At any rate, I don't think this was worth it.