Morn'n TimBeal,
...if they don't flush out it doesn't matter?
Yes, that's it exactly, (if I am understanding what "flush out," means in this context. With traditional line rule, (sometimes called "center line rule," here in North America because it is usually, not always, in the center of the cant) you visualize, design, and cut off a line that is actually deep inside the timber. This seems awkward at first, but once the method is understood, I don't know of any framer that I have taught, that does not start using it as there primary layout method, many exclusively.
From using it now my entire career, and the research I have done, it has been, and appears to be the dominated form of layout in the world. The oldest as well, second only to "scribe rule," which quickly changed to line rule in Asia millenia ago. This surprises many North American timber wrights, but least they forget, that in places like Japan, Korea and rural China, their timber culture is unbroken for thousands of years. Tooling, design and aesthetic is all off a middle line.
What happens if some wood is twisted or bowed while using line rule?
With out going on, as I can do, the simplest answer to this is nothing. Even severely twisted, bowed, and even a combination, plus taper-such as in posts, have no barring on you joinery, placement or function. It is as if it doesn't exist for the most part. When working with this method, (and the concert of support techniques that go with it,) the use of almost all timber stock, live edge, and log is opened up to the timber wright.
One of the best examples of late I can give is as follows. 150 mm x 250 mm (~6" x 10") principle rafter stock with over 50 mm of twist in less than 3.6 m (12'). This material was rejected and I bought it for less that $0.10/bf from a local sawyer. Once laid out and joint the twist was no longer apparent, unless you studied well the frame it went into.
This will, and the supporting techniques, are a large part of the manuscript I am preparing for publication. It is basically an English version of Middle Eastern and Asian traditional timber wrighting modalities, applied with modern tooling methodology. Their forum is so much easier to navigate and write on, that is where I spend the majority of my "log in time." They also attract a lot of "lay-folk" to the timber framing craft, so I enjoy the exchange and teaching. I have a piece on there explaining the basics of this method with photos. Hope this was of help.
Regards,
jay