Yeaaaaaa - I can't wait. Have you seen the plugin that decouples the slave axis, homes the A axis, and then recouples the slave axis. Interesting but I don't know if I trust it.
That is essentially how any gantry-squaring homing procedure works. All motors on an axis are started at the same time and with the same motion profile (accel, max speed, etc.) so that the gantry doesn't become more skewed while searching for the home switches. However, each motor stops when it hits its own home switch, regardless of whether the other motor is still moving. Once each motor is positioned at an identical distance (possibly zero) from its own home switch, the motors are "re-coupled". Usually this all happens in the plug-in or (more likely) in the motion device itself, and Mach4 is (again, "usually") never aware that the slaved motors have been effectively uncoupled and recoupled.
I think I remember seeing a thread somewhere (on the MachSupport forums?? I can't find it now) where someone had some Lua code that attempted to re-map the motors in and out of a slave axis configuration.
Bob