Mounting the Edge test bar between centers effectively cancels out any height error hypothetically due to the headstock not being level. However, before doing anything, I would remove the test bar and slide the tailstock up to the headstock until the two centers almost touch. You should easily see any height error as large as 0.042". As another check to make sure that your MT taper in the spindle is not the culprit is with the two centers almost touching but not overlapping, rotate the spindle 180 degrees. Or alternatively, with the test bar in place, position your dial indicator back over the headstock end of the test bar and check the runout. Or both.
I executed what you stated and found the tail stock center clearly higher. I checked runout on the center I had in the head stock which is 3mt then an adapter to 4mt for the spindle. It has .003 in runout. I dI'd notice I can see daylight through the two halve of my tail stock...hmmmm? I should probably start there and take it apart for examination.