As David said,
I would start by swapping the DBW motors polarity, the motor should drive to a closed position on startup to set the zero correctly, and it will trip out if the sensors read the wrong direction.
The main voltage going High to Low and vice versa on the tracking is not a concern, some OEM DBW throttles do this as well. the important thing is that they retain a linear trace, and the relationship between the two remains consistent.