Bob,
I read the diagrams/pictures on Sect 1, Sheet 20.00 a little differently. I think you are referring to the lower drawing and the seal cut-away on the right side of the door, above the lower hinge, labelled with a 2 and a 5 in a cube. That seal cutaway is, I think, to show that 3 oz of cement is required to seal the whole length of the door seal (under the seal). I think that the one butt joint is under the lower retainer, second screw in from the hinge side of the retainer (passenger-side door in this diagram).
On that page and on Sect 1, Sheet 28 (COE door - driver's side door in this diagram), the butt joint is in the same relative location; and, a butt joint is referred to (not butt joints - plural).
I do not know if my interpretation is correct but it is different from yours.
Tim