I found that a digital caliper worked best when I was verifying my X-Y-Z motions.
In the end the numbers came out exactly as one could calculate for the motor/pulley setups- 80/mm for X and Y and 400/mm for Z.
The width and thickness of the extruded traces will affect printed objects of course.
However IMHO they should not be taken into account for basic motion calibrations because their effects on the final dimensions of an object will change as a percentage of the overall dimensions of the object being printed.
Also, shrinkage of the plastic material will have an even greater effect on the final dimensions.
Those are best compensated for in the slicer software, not by changing motion calibrations.
Bed leveling would be a great candidate for a dial indicator I would think.
That must be adjusted fairly precisely to avoid adhesion issues.
And when all is said and done, a printed test object will tell you if everything is right or wrong.