I think you're probably right on the assembly jig. I can't think of another reason why the reference line would be below the body other than to eliminate negative numbers.
I just used the floor as a reference and did a little math to figure elevations of other points (or used other points to correctly position the new floor I put in.) But your wood frame would do the same thing, and eliminate the need to subtract any dimensions.
I did clamp a piece of angle on the front of the dash to use as a reference for the front cab support locations horizontally.
