Well, that's interesting, wizofoz. We never had that problem with EGPWS either in Honeywell or Collins equipped Global 6000 or Challengers. In fact, we had QRH procedures for using QFE. All designed with BBD, the avionics manufacturers and FAA.
One of my C-5 crews nearly CFIT'd in Bishkek. Had to convert millibars to inches, then QFE to QNH and then the altitude conversions. As Bishkek is at 2,000' ish, they couldn't crank down the baros low enough to indicate QFE. Now, the "glass" cockpit avionics can do that.