There is only one constant difference that I know of (if there are others I'd like to know what they are).
In the first image below is the two stamps without arrow.
In the second image below is the two stamp slightly enlarged with arrows pointing to the horiz. line that is on all of the Proprietary stamp and not on the any of the Documentary Battleship Revenue Stamps Series of 1898.
By the way, this horiz. line on the Proprietary Stamps appears in the same location, but on the left side.