I agree - the proximity switches might as well be removed. But the end-of-travel limit switches can be retained and used for homing in Mach3. I tried to also set them as limits in Mach3, but they're only on one end, and I must have had some noise in the circuitry, as they kept tripping out at inconvenient times. So Soft Limits are working for me.

Keep us posted on your progress!