I guess I'm not following all of that. One actuator rod per switch per axis is what I'm running. Here's a pic of the X axis switch assembly. There is a stop block along the front of the bed on each end to bump the rod and move the flag. The other two switches just have longer rods and a bracket that travels along the rods. Pushing or pulling the rods when contact is made. It's pretty much just like the IH system.
You've only got so many inputs on the breakout board for such things. I used 3, one for each switch. So, moving in a + direction or a - direction doesn't matter. I know what direction it was moving when it hit a switch and I know what direction to go to back off of it. Mostly anymore they're only acting as homing switches as I rarely hit a limit switch.
You can add more inputs by adding other boards, but I'm cheap and chose not to go that route. And like you say, you can wire them all into one input and they'll work the same. But the led's in Mach won't be right, if you care about such things. If and when I need more inputs I may go that route. Here's the little pcb I built for them. The twisted pair cables aren't mounted in that pic yet. These are just single sided pcb's. 2 diodes, a resistor and 2 switches.

I went with two optical switches per board for a reason I don't recall now. But I think it had to do with movement of the flag, or maybe not.
Bob