Is the paper "Field Wiring and Noise Considerations for Analog Signals" talking about AC or DC signal level?
They are referring to the amplitude of the signal, so the AC component.  Whether the signals themselves always stay positive, or have negative peaks, doesn't really matter.

The point is signal to noise ratio.  All they are saying is that you shouldn't use single-ended connections, with their inherent susceptibility to common mode noise, when the signal is less than 1 V.

This is clearly meant to be a rough guide.  For example, they are saying it would be OK to use single-ended signals for line-level audio, but not for microphone level audio, for example.