In my own experience using this tool, it is common to find that bullets from any given lot of quality manufacturer's bullets will vary a total of about 0.010"(entire range, not +/-). With bullets designed and engineered for precision, like the ELD, I would expect that to shrink even more.
I think what you are experiencing is common and I "think" I know exactly what you are having happen. It may be more prevalent with a less than clean chamber, maybe not.
When you get the modified case all the way into the chamber and start pushing the bullet with the wire, sometimes it gets a little "hung up" and seems to have stopped, but is not actually all the way to and touching the lands. Back off it a but and push it again. It could be dirt or a ever so slight rough spot that is stopping the bullet.
Pushing with that little wire, you will not physically be able to push hard enough on the bullet to mess up the measures by pushing the bullet into the lands. I will warn you that you will likely need to have a rod available to push the bullet out because it will stick to the lands. As long as you screw the wire stop down, that is not a problem. When you get the bullet out, just put it back in the case and measure. You should be very close on measures with all bullets tested.
Pro tip: use a bullet of a smaller caliber to make it faster popping that bullet out that is stuck in the rifling. Don't drop it straight down the bore vertically or you will mess up the bullet tip(and possibly your measures), but let it slide down at an angle.