I put a little note in the Tattoo section about this. I will try t answer this question for you.
The Flash in the point and shoot mode is totally configured and driven by the Auto setting. It meters, and then shoots. When you use your P or M function on your camera, the external flash can be set and synchronized with the body of your camera and you can actually dictate how you want flash to act. The latest flashes using TTL-II technology, where flash decides at what lens distance configuration how much light suppose to go out. Build-in flashes also have other functions, for example Canon 7D internal flash can take a role of a transmitter to all other wireless flashes. It would meter distance, synchronize all external wireless flashes and send command to fire. Some pro cameras like Canon 1Ds III don't have flashes build in at all. This is because these cameras are certified as weather proof cameras and built-in flash could be a huge problem for the certification. Generaly buil-in flashes are not used a lot in Pro photography and if you really want to control light get a good an external flash. If you do portraits a lot this is one think I woudn't save my cash on.
Here is a chit sheet for you to see how it works Flickr Photo Download: Portrait Lighting Cheat Sheet Card
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