Hi Mark,
That should work. Re-define the coordinate system.
The only glitches I can think of are that the Tool Setup | Trajectory Planner settings may need updating as well. If the axis resolutions, max velocities, max accelerations, Jog speeds are different for the different axes. You might want to create a different KMotionCNC Configuration for each mode.
Also the Jog Buttons may need to be re-positioned. For example Z jog buttons might be positioned to show left/right rather than up/down. The Lathe screen face might possibly work or a new Screen might be created.