My thoughts.
0). Hang the operator upside down. (LOL not practical)
0.1) Live with it and remain confused.
0.2) Was it worth moving the control. Was it ALL thought out? 12000 lbs. still can be rotated. Only the electrician,forklift operator and waste money department will curse.
LOGICAL SOLUTION but may not be practical.
1). Change the direction of the servos. PLC or hardwired. - Now the directions are correct.
2). Reverse the scales so that zero(s) are at the opposite ends. Or make scaling factor minus one and redo the machine offsets. Now the numbers go the correct way.
3). Swap the overtravel switches end for end each axis or reconfigure PLC.
4). Put the home switch at the opposite ends ends of X and Y travel.
Super X3. 3600rpm. Sheridan 6"x24" Lathe + more. Three ways to fix things: The right way, the other way, and maybe your way, which is possibly a faster wrong way.