Why is it important that the signals be close to 90 degrees out of phase? Here's why: imagine they're some smaller amount (e.g., 45 degrees). That means that there's a smaller time for at least one of the 4 states of the quadrature progression at any given speed. In the 45 degree case, it makes the maximum accurate count rate only half of what it could optimally be for a perfect 90 degree phase differences.
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