Hi,
It's quite simple really. Mach3 homes one axis at a time. So as it homes an axis, and the input with the X/Y/Z in series switches is activated, it can only be the switch for that axis that caused the activation.
If the machine was homing the Y axis for instance, and you manually pressed the Z home switch with your finger, Mach3 would incorrectly assume that it has hit the Y home switch.
If the same switches are used as limit switches, Mach3 doesn't know which axis tripped the limit switch input as multiple axes are in motion. It doesn't care as it just EStops the machine.
Cheers,
Peter