I believe I know just what you're talking about because I had the same situation on my '48.
The connecting rod doesn't follow the contour of the door (that long channel), although common sense would tell you it should. You'd have to install the mechanism upside down for it to follow that channel in the door, but then you wouldn't have a hole for the third bolt. Have I got it right?
I have two books that illustrate this mechanism. The first is a factory piece entitled "Servicing Chevrolet Truck Cabs (1947-1948)" In it is presnted several pictures showing the connecting rod in that channel, with the connecting rod coming off the bottom of the mounting plate. (The connecting plate is shaped like a pyramid.) The mounting plate has the pyramid connecting hole in the proper orientation to make the connection this way. However, as we both know, our mechanisms have the connecting rod coming off the TOP of the mechnism, at the point where the top bolt is on that pyramid.
My other source is the "1947-1954 Truck Factory Assembly Manual." In it, (Section 1, Sheets 1.05 and 1.06), the illustrations clearly show the same mechanisms we have - with the connecting rod coming off the TOP of the pyramid and descending slightly downward to the latch. The connecting rod crosses over the channel about midway across the door.
I'm assuming that GM originally had a design for the connecting rod mechanism that went through the channel, then changed things after they printed the "Servicing Chevrolet Truck Cabs" booklet, but before the trucks went into production.
Does this clarify things for you?