Is it possible that because the z axis is not all wheel drive (3 motors) but rather a single motor driving a belt to all 3 points plus a 4th added point from the auto tensioner that the z rods are not moving at exactly the same rate ?
That alone may cause some discrepancy in the accuracy of the 3 points of movement
You could use your leveling design that you graciously put together and install it on all 3 bearing tops as a test
It wouldn’t surprise me if you find the corner with the discrepancy is moving at at different rate than the other 2 