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It doesn't matter where they break as long as they don't keep the throttle fully open till the point where the speed is measured. And since those points have to be chosen early enough that even MotoGP riders aren't on their brakes there yet ... well, your argument is invalid.
Also, you get the best indication of engine power at the end of the straight (as has already been pointed out) since mass of the riders and other aspects play a bigger role earlier on the straights. If a rider accalerates out of a corner better, he will have an advantage at the beginning of a straight, but that advantage diminishes the longer he has been on a straight.