Personally I don't see the issue with laying out the timber in the drawing, if I am understanding it correctly. I house all my joinery, so if I had a timber that was way out of square my housing would be deeper on one side. The exact depth of the housing being determined by it's distance from the snapped line. So in a typical frame all of the similar timbers are interchangable, as with square rule. However, the snapped lines give far more detail to inform the joinery cutting than square rule.
To use the example of the OP, it wouldn't matter to me a bit if a timber was out of wind. All the joinery would be perfectly plumb and level to one another regardless of the timber.
Another benefit that I have found using line rule is that it makes a handy reference for planing. I plane my timbers after all the joinery is done, right before it goes out to the site. All my joinery is housed, so the joinery is not affected.Ends where they enter a housing need to be exactly sized in planing, and the lines are great for that.
Hopefully that clarifies the matter, let me know if I missed anything or was not clear enough.