I'm not too sure about the F16's altimeter, but I can't wind 100 millibars (3000') of pressure off the altimeter in my jet in order to get a QFE reading with an elevation of 3000'.
And before anyone brings up the Rad Alt idea - they don't work very well in looping manoeuvres.
A gate height is a gate height. It shouldn't matter what pressure stting you have, as long as it's the correct one.
Reichman