You're method is quite alright - BUT -
Don't take this as a criticism, but I don't see what adjustment you can make.
To start with Mach 3, a 1 inch movement is governed by the steps per unit you enter in Motor Tuning. This is not something you measure, or adjust, it is something you have to calculate. I know you can get Mach 3 to do it for you, but that depends on you measuring something, and therefore is open to error.
Steps per unit is a multiple of :- Microsteps (set on the motor driver card e.g Gecko = 10), Steps per revolution of the motor (1.8 degree motor = 200), any gearing gown to drive the leadscrew (mine is 3), and finally turns of the leadscrew to move one inch (mine is 10). The answer for my motors is therefore 60,000 pulses per inch (Not 59,945 or 60,021 - which I might get if I resort to measuring). You can see that I have 60 pulses per 1000th of an inch. I cannot measure that small, therefore I must be innacurate.
Your secondary digital readouts will have an accuracy printed on them, but the digital calipers I have are fixed - I cannot adjust them. Whether you can with yours, I don't know, but of course - if you are adjusting them - what do you use as a measure.
My steps per inch are accurate, and I measure them with by digital calipers and usually get to 1/2 a thou, which is as accurate as I can measure with the equipment I have got.
If you used Mach 3 for your steps per unit, then calculate it out instead (it should be a round figure like 60,000) unless your leadscrew is metric or something, but even then you could set up in metric if that was the case - and still settle on a round figure.
Once you get your step per unit correct, Mach 3 will be accurate, unless your motors miss steps, and this to me is where your second DRO comes in. If your motor miss steps, then Mach 3 will say, put out 60,000 pulses, but you motors might receive only 59,750 meaning that the actual movement is just over 4 thou short - and this should be picked up on your second DRO.
Other than that, I would have thought that the two DRO's should match - within the tolerances of your second readout.