To continue...One advantage to the chalk line is that you have good registry for the framing square. The alternative is the eye ball method. Suppose you have a timber that has an uneven surface, you cannot register the square on the side of the timber. Place the square with the long leg on the flat surface with the outside of the square roughly aligned with the side surface, sight down the square and align to the shaft. I have squared around some nasty stuff using that method.
The important thing to remember is that all workable and repeatable method (square, scribe, mill, jigged bench or CNC whether numerical or relational) operate under the same set of rules, albeit expressed differently.
Roger