I agree with you….the shadow of the brake wheel is almost parallel to the axis of the car and the shadow of the “too tall brake staff” should be visible aft of the brake wheel on the coal. It is not, suggesting that the rod is actually stuck in the coal load above the CC&StL stencil.
Charlie Vlk
One other possibility is that what appears to be the upper portion of the rod is actually a rod embedded in the pile of coal against and inside the gondola end and the angle of the photo made it appear as an extension of the brake shaft. It seemed strange to me that this extension is above the nut and a different diameter than the shaft. .