As for transferring the design into the real world, I.E. making an actual building with the proportions represented in the drawings, there is some degree of difficulty.

The lines on the graph are 1 dimensional. They have only length, and as such they cannot account for the other 2 dimensions of actual wooden timbers. The lines merely mark centers and intersections, they do not really tell where a timber 'is'. We run into the greatest difficulty at joints where timbers do not join at the same height, for example in an English tying joint, or certain rafter joints. In such instances, you have to come up with a way to account for this variance.

To convert your building from the 1 dimensional lines of the graph to 3 dimensional reality, I can think of 2 methods. The most obvious method is the French Scribe method. Here we simply take of design and enlarge it, creating a full-scale version of it right on the ground, using strings stretched across or some such method to represent the lines off of the design. Then we are free to align our timbers with these building lines and scribe our joints onto each other. Observe, however, that these lines usually represent outer edges and not necessarily center lines running down the middle of timbers. For example, the lines for the walls should be taken as representing the outside of the posts, and a horizontal line should represent the bottom of ties and joists. The main reason to do this as I see it is so that, assuming you set your dividers so that standard measurements would result in the final building, predetermined distances such as building width and interior ceiling height will still retain their imperial measurements (or metric, if you absolutely must) For example, on my building I set the dividers at 4" so that I could have a ceiling height of 8 feet, and a total length of 24 feet. If I do the layout as described then My building's length should measure exactly 24 feet from end to end, measuring from outside corner to outside corner, and my wall height should measure exactly 8 feet from top of floor joist to bottom of ceiling joist. Note that should you decide that you would rather have your wall lines mark the inside edge of your posts, then you are going to run into a lot of trouble once you start running your rafters.
Another reason to do it this way is that it allows you to use irregularly sized timbers. In other words, all of my timbers do not have to be exactly 6 inches wide (I use rectangular, rather than square, timbers, so they might be as narrow as 4 inches at times, with a depth of 9 inches or more)

Now I was just thinking about 2 story buildings. In this case you may want to make an exception to the rule of layout lines marking an edge rather than a center. If you don't line up the first floor joists with the line marking the center, then the second story is going to be several inches shorter than the first. If you do, then both stories are going to be a little bit shorter than the ideal size. So It's a matter of choice, would you rather have A nine foot first floor and an 8 foot second floor (which would result if you laid out your building to have 9 foot ceilings, aligned the bottom of you joists to the line, and use 12 inch joists) or 2 8'6" stories (same layout for wall height, only the 12" joists are aligned with the line marking their center)

Really the only rules that I would set in stone are that: Building lines mark the OUTSIDE of posts, and roof lines mark the BOTTOM of rafters. It might be beneficial to actually have one or two lines here and there be a center line, with others marking edges.

There is another way to do it that doesn't require creating a full scale layout, so that you can cut all of your joinery in a smaller area like a cluttered shop or a crowded city lot. I thought of this one day while taking a shower -I doubt I am the originator of this idea, it's probably a way that someone used hundreds of years ago, but I had never heard of it that I remember.

Basically the idea is this: Take a given framing member, let's say it's a post. This post s stepped off for length, the length being set to the full distance between the two lines it is bounded by on the drawing. Note that the space between the bounding lines is not the same as the actual length of the post. Add a little extra yet for good measure.

Then any other timbers that join this post should be matched up and scribed and so forth. Let's say there is a plate running along the top, and on top of that is a tie beam. All three of these timbers need to be scribed together right now, aligning the bottom of the tie with the mark on the post for total ceiling height. Here you will glad you left some extra on the post, because it may tenon into the tie just a little bit, in which case the post would actually be longer than the distance between bounding lines. It will also need to tenon into the sill below, in which case even more additional length is added, assuming that the top of the sill is aligned to the bottom bounding line of the structure (to maintain interior wall height)

To do it this way, you'd have to have a lot more faith in your ability to step thing off correctly, because you don't have a nice big layout to constantly reassure you that everything is right.