and one question that pops up often enough is this scenario
To be honest, I think this is far more rare than you may think. I've been following this forum for about 10+ years, as well as other forums where Mach3 is used by a majority of the members, and I think I've only seen a machine like this maybe twice?
Mach3 has no special support for this, so it's up to the user how they set up the machine. It's either setup like a traditional machine, with the horizontal spindle moving up and down, or the Z axis becomes X or Y, with the gantry moving along the Z axis. (Basically just rotating the machine 90°)
With the first, getting g-code from a traditional CAM program would be very tricky. With the second, it's just standard code.