Ok
Mach doesnt care, if it sees a limit it E-Stops so if you have separate switches the only benefit is you can look on diags page and see which switch has tripped, in reality its just as easy if not easier looking at the machines position to determine that.
The only disadvantage of using all separate inputs is you quickly use inputs up , if using the parallel port this could be a problem as you only have a limited amount of inputs and that is why most have all switches wired NC and in series, as they only use up one input.
Not sure how your bob works but you will see if the switches are working on the diagnostics page, when the switch is pressed the LED should light and when released the LED will go off. If the LEDs for them are lit when they are not activated and off when they are, you will need to change the active low setting in ports and pins.
Hood