Measuring impedance of a DCDC converter
"How does this work?" 

It seems like you've got a pretty good idea of how it works. The basic idea is simple. Perturb the output with a frequency swept source, and measure the output current and voltage with a vector meter (Network Analyzer). Then have the Network Analyzer divide voltage by current (\$V_T\$/\$V_R\$), resulting in a plot of dB\$\Omega\$. 

How this all gets accomplished will depend on the DUT, Network Analyzer, and some other particulars. Most of the time, for converters with low output impedance it is beneficial to use a Linear Power Amplifier to drive the output. 

A lot of Network Analyzers can't accept the DC voltages that a directly coupled \$V_T\$ would see, so often that ends up AC coupled. Usually it can just be hooked to the AC side of the blocking capacitor. 

A current sense transformer can be really good to measure current with, rather than a 1\$\Omega\$ resistor. Those like you would find in an EMI lab work pretty well. 

It's a good idea to have a test impedance (resistance) that is close the the lowest impedance that will be measured, so the instrumentation error can be zeroed out in the Network Analyzer. 

The Network Analyzers are pretty good a rejecting noise since the receivers track the oscillator frequency. But, there will be some noise. To some degree that's just part of real data. Usually some noise is present at the switching frequency and some of the harmonics. You mention ripple, but a lot of what gets called ripple seems to be common mode noise. You might have noticed in Figure 16 some beads on the lines to the NetWork Analyzer. That's going to be about common mode noise. It depends on the frequency, but for the stuff around 2MHz to 10MHz, beads may not be enough. For those mid-MHz frequencies a common mode choke would be better. Something with about 1mH of inductance. Or, just wrap the Coax lines around a EE ferrite core.