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If you look at the documentation appendix g on page g-12, there is a diagram at the top of the page that gives the logic of the sensor. It was intended for positive or negative logic and outputs both a positive and negative signal so the user can choose whichever meets the needs of the system. The bottom line is that the outputs will always be opposite unless your sensor is broken. You are correct in saying that it wastes a digital input but only if you've reprogrammed the controller. The way it is set up for the default program, and the example of pins 15 and 16 there is an assumption that the condition of the sensor either disables relay 2's forward bias of the voltage or reverse voltage bias of the voltage depending on the state of the sensor. This assumes that you will always want to disable one condition and allow the other. Reprogramming the controller would be necessary to allow disabling relay 2 for either forward or backwards bias OR enabling forward AND reverse biasing at the same time.
OK, final point, referring to the diagram on g-12. The reason for connecting both outputs...if the outputs have little output resistance, you risk shorting the power supply to ground which means your sensor becomes an odd shaped fuse and burns out. However, you've asked a good question and it's probably one that you could forward to F.I.R.S.T.... just be sure to insulate the unused output.
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