The direct-digital phase noise measurement technique is described in "Direct-Digital Phase-Noise Measurement" by Grove (DOI:10.1109/FREQ.2004.1418466, PDF link). The basic architecture of this technique, for 1 DUT and 1 reference channel, is shown in the following two block diagrams.
In the 2nd image, the "Sample and Down Convert" block is the block diagram in the first image.
In that 2nd image, the reference phase is scaled by the ratio of DUT to reference frequency. Why is that done?
Here's my understanding of the signals and noise terms. Consider an input DUT signal:
$$ \begin{equation} x(t) = a(t) \cos[\omega_{\mathrm{dut}} t + \phi_{\mathrm{dut}}] \end{equation} $$
When this is sampled by an ADC it incurs additional phase noise due to sampling clock jitter and ADC (mostly quantization) noise. Therefore, the signal after the ADC (ignoring its discrete nature for now) is
$$ \begin{equation} x'(t) = a \cos (\omega_{\mathrm{dut}} t + \phi_{\mathrm{dut}} + \phi_{\mathrm{adc}} + \phi_{\mathrm{clk}}). \end{equation} $$
To demodulate this signal to baseband, we multiply it by a quadrature NCO signal
$$ \begin{equation} n(t) = e^{i \omega_{\mathrm{nco}} t}. \end{equation} $$
The result of this multiplication is
$$ \begin{align} x'(t) n(t) &= a \cos (\omega_{\mathrm{dut}} t + \phi_{\mathrm{dut}} + \phi_{\mathrm{adc}} + \phi_{\mathrm{clk}}) e^{i \omega_{\mathrm{nco}} t},\\ &= \frac{a}{2} \left[\exp[i (\omega_{\mathrm{dut}} t + \phi_{\mathrm{dut}} + \phi_{\mathrm{adc}} + \phi_{\mathrm{clk}})] + \exp[-i (\omega_{\mathrm{dut}} t + \phi_{\mathrm{dut}} + \phi_{\mathrm{adc}} + \phi_{\mathrm{clk}})]\right] e^{i \omega_{\mathrm{nco}} t},\\ &= \frac{a}{2} \left[\exp(i [(\omega_{\mathrm{dut}} + \omega_{\mathrm{nco}}) t + \ldots]) + \exp(i [(\omega_{\mathrm{nco}} - \omega_{\mathrm{dut}}) t + \phi_{\mathrm{dut}} + \phi_{\mathrm{adc}} + \phi_{\mathrm{clk}}])\right]. \end{align} $$
The $\omega_{\mathrm{dut}}+\omega_{\mathrm{nco}}$ term is at a high frequency and is filtered out. This leaves
$$ \begin{equation} x'(t) n(t) = \frac{a}{2} \left[\exp(i [(\omega_{\mathrm{nco}} - \omega_{\mathrm{dut}}) t + \phi_{\mathrm{dut}} + \phi_{\mathrm{adc}} + \phi_{\mathrm{clk}}])\right]. \end{equation} $$
We can extract the phase of this from the 2-argument arctangent function, leaving
$$ \begin{equation} \phi_1 (t) = (\omega_{\mathrm{nco}} - \omega_{\mathrm{dut}}) t + \phi_{\mathrm{dut}} + \phi_{\mathrm{adc}} + \phi_{\mathrm{clk}}. \end{equation} $$
If $\omega_{\mathrm{nco}} = \omega_{\mathrm{dut}}$, $\phi_1 (t) = \phi_{\mathrm{dut}} + \phi_{\mathrm{adc}} + \phi_{\mathrm{clk}}$ (this won't in general be exactly true, but I think it's ok for this analysis).
If we did this for the 2nd channel too, we'd have
$$\begin{align} \phi_1 (t) &= \phi_{\mathrm{dut}} + \phi_{\mathrm{adc1}} + \phi_{\mathrm{clk}},\\ \phi_2 (t) &= \phi_{\mathrm{ref}} + \phi_{\mathrm{adc2}} + \phi_{\mathrm{clk}}. \end{align} $$
I don't see anything that indicates those phase terms depend on the carrier frequency and need to be scaled prior to subtraction.