Are you sure both pairs of wires aren't for 1) A reverse lockout and 2) reverse lights?
I would be surprised if your transmission had any sort of neutral safety switch in it, manuals cover this safety feature by using a clutch safety switch.
Wiring for the reverse lights is similar, the power going to the reverse lights on the a/t goes through the NSS, they'll need to be snipped [typically the outer two wires] and simply connected to the reverse switch in the trans. Which wire goes where is insignificant for that.