This is also my field. The issue is, the machine will be repeatible on the short term but not on the long term. It will look like it's behaving well during calibration and the next few months of operation.
But if the ways and mating surfaces aren't almost-perfectly straight and flat, they'll experience accelerated wear. (If you're using hydrostatic bearings, they won't work to begin with unless the surface is accurate). Then the calibration is gone. And that's just in the static case.
If your ballscrew has uneven pitch, is eccentric, or any number of other issues, you can calibrate it out. But now to move at a constant speed, your servo controller has to drive that inertia at a wobble, and everything shakes.