Because an NEJE machine has a diode laser, the focused laser spot is rectangular, despite what the manufacturer may claim. If the diode is oriented to put the rectangle’s long side parallel to the Y axis, the machine will produce a wider cut along paths roughly parallel to the X axis.
A wall test will reveal the spot shape and orientation:
The focused spot will be on the order of 0.1 mm = 4 mil wide, so maintaining tolerances smaller than that will require exceedingly careful calibration, adjustment, and operation. The rectangular spot shape will produce different results in different directions; there is no way to correct that through LightBurn settings.
You must calibrate the motion using lines marked on the surface, not cut shapes, to exclude the kerf from the measurements: