You can in fact fudge the parameters for travel on any of your axis's. I would personally recommend against doing so. You can only get a very small amount before you start causing damage, I thinks its about .1 on x and y, not sure about z tho.
The parameters are set by the number of encoder steps so the number to enter is dependant on your ball screw.
Again I would recomend against messing with that, and its very odd that your handle jog allows you to travel to a distance that produces an alarm, that may actually be a problem to have looked at.
Probably use a longer necked holder or get a extension with a small collet on the end of it.