The point is, the original factory parts didn't fit into those recesses.
I don't know why the inner panels were stamped that way unless they were a hold over from the '46 and earlier models which had different door hardware.
I believe that they did fit in those recesses in in the earlier ADs, when the inside handle was pushed forward to open the door. They were changed in later model years to a pull-to-open configuration, requiring the glued on spacers mentioned above, to clear the cardboard door panels.
Carl