It could also be that in order to shoot longer distances you naturally have to anchor just a bit different and may be looking through the peep just a little different---because of the angle for shooting that far.

I know I used to do this when shooting field. I had to adjust my peep for short distances so I was looking through it on the high side so that I was looking through the center for the long shots. It wasn't much, but it did make a difference.

Now whether this has any bearing on the sight marks I couldn't say. That was over 30 years ago and my brain doesn't function well with the past. Too busy living today.