Meatzardd, i've recieve my aluminium tranny case yesterday and me too, on the thin plate who bolt under the tranny, the 4 hole was not counter-sunk.
I've take a drill mesh and couter sink it myself, but as you said, it's bizare that FLM have forget it, and as i can see, it's on a lot of them that they forgot it. :032:

And the bigger locknut is for secure the crew who hold the arm mount in place. Don't know why, because the arm mount is ever thread, i suppose is for give an extra security.