I was thinking about it like this, the top clamp and the top of the forks are in the same spot relative to the frame, but the thicker washer is causing a bigger gap between the top and bottom clamps. So the line on the fork tube is the old resting position of the lower clamp and I believe we are seeing the difference.
I didn't put the forks on until after I had tightened everything down. I am pretty sure I only got about one turn out of the spanner nut though, even though there are 4 threads showing. There are those teeth on the bottom of the spanner nut, the height of maybe 1-1.5 threads. I will take off the top clamp and look again tomorrow.