If you haven’t built a machine before it’s easy to assume that the steppers are like regular motors and will spin on and coast down to a stop allowing the axis to sail on a bit. But as Neale says they only move if they get a series of step pulse signals. If the pulses stop then the motor pretty much stops dead and (someone jump in here!) is held in position by the coils being energised in one place. In fact Estops make a bit of a mild bump/bang as the stop is so quick so you only do it when called for. I’d be surprised if they overshoot more than an 1/8 of a turn and probably less.
The estop is so fast that under normal conditions it is kinder to the machine to use a software accel/decel ramp. What looks like a soft ramp up to speed and soft ramp down to a stop is actually the motor following the ramp parameters you asked for in the setup, not an uncontrolled overrun In MACH3 this is easy to do and other software no doubt has this as it is required for nice machine control.
So to cover all bases (homing and fast jog) maybe allow 10mm between home and limit. Make the home adjustable and you can claw some travel back once built and tuned.