The Billy Cook saddle is a wood/hide tree. I've looked at those before. I agree the right rear inside of the bar is were the rub mark is coming from. A few things could be causing that. The rear part of the bar doesn't have enought angle on them. So all the pressure is on the inside of the bar. Your wither pocket is to wide for that saddle. So that is causing a saddle to sit to high in the front. There by causing a bridge in the center of the saddle. That would cause to much pressure on the rear part on the saddle tree. And the rear bars could be to close for your horse. All these problem would show up more when running then walking. You may give him a brake from running for a away. See if the hair grows back. Changing the pad may help the problem not be as bad. It's hard to tell in a picture. That's just my opinion. I would bring your horse and saddle to the nearest qualified saddle maker and let him look at it. After seeing it he may have some suggustions. In the end you may have to get a saddle tree made to fit your horse correctly. And then get a saddle maker to do the rest.
I had a problem with my Billy Cook. My horse grew to big for it.
It's three things that cause back problems the horse, saddle or the rider. Here is a interesting article to read about saddle problems.
Saddle Fit by Dusty Johnson
Mort