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The sensors in serial mice have two channels (already at appropriate distance), so there is no real need for arrangement like on your wheel.
Also, the sensors must be positioned (and they are) such that when one is at the centre of the track (black or white, doesn't matter) the other one must be between the two (just changing state).
This is called quadrature position, and this is how mouse (and Ek's box) know in which direction the wheel is moving.
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