Well I'v read through both alignment methods,one with tool and one with straight edges.
As the box and swing arm are attached to the rear mounting I'd guess the tool pushes in the same amount each side to centre the rear mount in the frame.The links are then adjusted to hold engine/box in the central position so the bolts just slip in to eyes.
Using the straight edges instead of the tool the links are use to pull things into line until front and back wheels are lined up.
That's the best I can come up with without poking and proding the actual bike.
