....snip...As noted, tailstocks on new machines are (generally) a few thousandths "high"- this allows for some of the inevitable wear, where the tailstock will eventually wear down to perfect alignment, and then continue wearing and getting lower, until one needs to shim to get it back to correct height.....snip....
Measure the vertical offset of a new lathe quill centerline compared to the spindle centerline cold and then remeasure after running it at mid speed for 15-20 minutes. You will probably find that the centerlines are much closer/dead on. The reason for the tailstock quill centerline being higher the the spindle bore centerline, in many lathes, is to compensate for thermal expansion of the headstock once the machine is at operating temperature.