Good points WM & smallblock.
Here is my suggestion: The DRO's will have calibration setup. The Jensens all do. When you have the dial gages setup for X and Y. You move 1". When it's exact as possible, and repeatable, you then check the DRO. If the DRO does not read 1" you will enter the DRO's offset Cal screens. They will have you complete a process to "calibrate" the DRO and scale it to the measured movement. Once you have that. you then tune Mach3. Move 1" and get Mach3 tuned to 1 inch. It's what I have to do and it came out much better overall...
points: As noted- Mach3 is not a closed loop system like Servos. missed Steps and exacting 1:1 moved on DRO and Mach3 simply is not going to happen (all or most of the time).
Once thing many do: Use of Servo systems and DROs are much better- But still have DRO to Servo/Encoder/Backlash errors. Many put on "magnetic encoders" and feed that into the Servo Drivers/PLC inputs thus replacing the encoder pulses. This means you are not measuring the distance moved via motor encoders, but actual distance the table itself is moving. It's something I want to try w/ linux CNC and scales if I could.... Someday.
Mach 3 cannot perform this type of work thay I know of. There are micro-step server systems as closed loop stepper systems but I have not researched how they do what they do and if Mach3 can even get into managing any offsets ir missed steps.
ENJOY your new rig!