I see your point about how one limit switch input could be connected to both limit switches and have the same operation. The two inputs have separate LEDs so you know which switch is tripped. This is especially useful for troubleshooting if a switch has failed.

With computers and electronic drives there are faults which could cause unintended motion in either direction so it's necessary to disable the drive if either limit switch is tripped.

In the old days of relays and reversing motor contactors a limit switch could safely stop travel in only one direction. Equipment where crashes would be dangerous or expensive had an additional set of limits that killed the drive power if the first set was passed.

If I understand the question I offer the following ..
I have two switches per axis, each wired to separate input pins, 6 in all. Three of them are also designated as home switches in addition to the limit function.
Any switch active stops the machine complete, so that behavior is normal.  In that sense the controller doesn't care which switch it was ... they all stop the machine.
Since the inputs are different though, a readout display on mach4 shows which switch was activated. To clear any limit event I hit the limit override button, jog the machine off the switch, and restore the override to normal.
There is no chance of the limit switch reactivating while the override is in effect, and indeed jogging in the wrong direction will go through the limit switch point.
I have the override button flashing while activated to help me remember to turn it off when the limit is cleared.
I hope that helps.

There are 3 inputs for each Axis, 2 limits and home. Your description of the limit switch operation is correct. The home switch can be anywhere along the allowed travel. The home switch is only used when performing the homing operation which sets the machine coordinates.

There ways to operate the machine without some of the switches.
The home switch input and a limit input can share a switch but that's often not convenient as you then have to travel to the end limit each time you home the machine. 
You could have only a home switch and use soft limits to stop travel at predetermined points on the machine coordinates. If a fault causes the actual position not to match the computer's position a crash can occur.
You could add a home in place button instead of having a home switch.