I believe that you have it correct. Since the holes are at an angle, when the holes are made through both sides at once the slant will be correct for the front side, but incorrect for the back. This results in a great looking front, but a not so great looking back. If the holes are made in each side separately, then both front and back have holes at the correct angle for their side and stitching on both front and back will look good. You can see an example of this in Nigel Armitage's video on YouTube where he reviews the Crimson Hides pricking irons. At the 27 minute mark, he makes the holes in both pieces separately and then puts them together and stitches. He then challenges the viewer to decide which is the front and which is the back.
Of course, if the back is not going to be seen there is no need to go through this extra effort.