All coils have mutual coupling (you mention a rod). The generator output (V1.pos) should be connected to CH1 as this is your source. That should still be a square wave, unless the generator cannot drive the impedance formed by the two windings primary winding. With a high enough coupling factor (>0.9 which you most likely do not have) the generator sees the 50 Ohm scope load parallel with C1.
What kind of impedance you have between V1.pos and net scope should be easy to plot. You will be surprised to find out what the actual transfer is (I expect a peaking around some frequency). The square wave at V1.pos (the gen output) might be completely distorted and only show narrow needles, it does not matter for the transfer calculation.
The normal application is to measure open loop transfer by placing only L1 in series with the feedback path of the control loop. L1 generates some signal and you monitor L1.pos and L1.neg on CH1 and CH2 to plot the loop transfer. At very low frequencies all signal will be seen on CH1 (the low Ohmic output of the LDO/DCDC) while at very high frequency all signal will be seen on CH2 (connected to the feedback point error amplifier). At some frequency the two channels have the same amplitude. That's the 0dB point where you want to know the phase. That phase is your phase margin.
I found two small unknown transformers that I measured. I connected one winding to the generator and CH1, the secondary winding I connected to CH2. The transfer is as shown below:
Transformer 1

Transformer 2

This shows how easy it is to detect that the gain is 15dB (voltage out/in = 5x). It also shows that the transformer is usable up to 350kHz/100kHz. At these frequencies the transformer starts to self resonate. Above the self resonance frequency the output drops by about 40dB/decade as expected. The requirement for the transformer is very low. As long as it can generate a signal above the point you expect the loop gain to become zero.
A 5:1 transformer is fine as the generator can drive one winding with 0.5V to deliver 0.1V into the control loop. And 0.1V step is assumed to be within the LDO/DCDC output voltage control range (5.05V and 4.95V for instance). CH1 of the scope will start at low frequencies with 100mVpp which can easily be set to full vertical range. CH2 (the error amplifier input) will hardly see any signal as the feedback will remove most of the signal. CH2 vertical range will be set to perhaps 1mV/div. This assures that the dynamic range of this measurement will be 120dB (80dB scope and 40dB due to the change in vertical settings of the scope).
This is just the theory I have in mind. Still need to find a regulator to try it on
