Because of the motion ratio of the suspension geometry you can't directly compare distance from a bump stop to total wheel travel. If you know the motion ratio you could do the math but its not going to solve anything without knowing the compression limit of the bump stop.
You mentioned the tires are the same as OE sizes, but every manufacturer makes tires slightly different within the same standard tire size. Look up the actual overall diameter for your original factory tires and compare to the actual diameter of what you have. More than likely they're slightly taller which is why they rub, but it doesn't appear to be doing significant damage just very light rubbing, which I wouldn't be concerned about.