Paul, most better flash units have Red light/Infrared emitters that created a cross hatch light pattern that really helps the AF system by providing bars of light that have high contrast edges. The white light emitter on the body is not as effective and it causes a person's irises to close, and it distracts them and changed their expression. The flash mounted assist light turns off the body focusing assist lamp. In dark conditions, very good focusing can be done with the AF that is impossible to manual focus accurately in the dark.
Much of my shooting in performances, dance clubs and other shooing conditions that requires focusing assist. I never use the body white assist light, nor do I ever use a pop up flash. I have 3 SB900 flash and 3 Yongnuo YN-568ex flash. The red+infrared focus assist light on the YN-568's is brighter and has more cross bars, but both type are very effective in focusing in the dark.
Back when shooting film, manual focus was a dream...assuming decent light using the micro mesh focusing screen, and only in the center of the frame.