Indeed, a flying 100 is not 100 meters of effort, it includes the wind up and acceleration. But if you are negative splitting your 200 (as I am sometimes known to do...) you didn't get the first 100 right, you needed to be faster quicker. The best 200's are always fading slightly in the second 100. It's all necessary, of course, and you can't get your top speed by doing only rolling half-lap accelerations (but there's a place for those too...). Rolling 500's are a staple of mine, but I don't consider them to be top speed work.
Nuts and bolts- reduce fade in your 200 by doing flying 300's. They are painful.