Nothing is square in boats, except for reef knots. My carpenter friends who are on the level might have difficulty here. Engineers seem fine with the angles, but have trouble determining tolerances. Architects are used to building on a firm foundations but even the earth moves in slow tectonic waves. Seismic ones are faster and violent.
You could say there are parallels in building since the a-cats are stick built, made of many smaller forms comprising the whole. The precis is different. Boats are only temporarily land bound; they are designed to be water creatures supported by the buoyant force of the water mass they displace. The ends of the sticks come together in odd joints which must take into account species and grain.
Here John is setting up a deck beam, a supporting member for the deck whose joints with the hull will combine to create more support for the mast and a tight stiff smooth structure to transmit the driving force of the sail. Notice the intricacies of the joint, It must match the curve of the beam with the curve of the sheerstrake, be flush with the oak frame it abuts, and sit firmly on the sheer clamp.
Many kit boats are cut on computer using cnc routers with step scarfs and other niceties. I've put a few of these together. I like the kit-ness of them. Kind of like your it house idea. Some building methods like stitch and glue, don't require joints at all. They use an engineered lumber product and sheet shapes to create form. The epoxy filler and glass or carbon tape creates the joint. Other building methods use strips of solid wood with cove and bead moulded edges, glued together over the molds. This creates a very light hull which is then covered with carbon or glass to form a composite structure. Both the above methods could be as green as traditional practices.