The help says:
Z-Axis Scaling— Adds a visual extrusion to the board stackup to better view internal structures and displays barrel holes of vias. Does not affect the measurement tools which report true values.
The effect of Z-Axis Scaling is to show the PCB scaled according to the scale factor which is at least 2.
It looks like there is no way to show the holes without this Z-Axis scaling which deforms the image.