Differential and Common currents in EMI Design
The below picture should shed more light on the way these currents circulate in the circuit:

The differential-mode currents can be quite easily predicted with a simulator considering the below scheme while common-mode types are more difficult to predict/model as they involve PCB layout, stray capacitance with heatsinks (if any) or inter-winding capacitance for instance:

You will need dedicated receiver and line impedance stabilization network or LISN to assess the level of noise. Please note it is best to combine signals coming from the LISN line and neutral outputs to isolate differential- and common-mode contributors.

The LISN is there to fix the grid output impedance to 50 ohms from 150 kHz to 30 MHz. That way, measurements performed in France or in the US are done on the same grid output impedance.
Disclaimer: I plead guilty for writing the application note you referred to. I was wearing short pants at that time : )