You do not have X and Z home switches set up so they will not home
All that will happen is Mach will set machine zero for X and Z in the position they are sitting at when you press the Ref All button.
When you reference the machine that sets the machine zero coordinates and because of that Mach knows you are at the machine zero position and thus knows the size of table due to the numbers you have entered into Homing and limits.
If your home is at a position other than X and Y fully negative and Z fully positive then you will need to enter a Home off value so that Mach knows how far it is away from machine zero when homed.
Hood