I calculated the MC open loop transfer function with the combination method. For that, I made a circuit model of the MC board (from the input to the output). The transfer function of this circuit is calculated by SPICE (attachment1). Then it is multiplied by the measured transfer function from the output of the MC board to the input of the MC board (attachment 2) to get the overall transfer function.

The result is shown in the attachment 3. The blue curve is the OPLTF measured with the traditional method. The red curve is the combination method described above. There are some discrepancies between the two curves. The ratio of the two curves (Traditional)/(Combination) is plotted in attachment 4. It seems there is a pole(s) missing from my model of the MC board at around 1MHz. This may come from the omitted op-amps in the MC board model (there are so many op-amps which have flat responses below 1MHz and I omitted most of those). Also the MC board includes many generic filter stages to customize the frequency response. I will open the MC board box to examine what is actually implemented on the board. 

At low frequencies, the two curves are similar but the slope is still different.

I also had to add 83dB of gain to the combined TF to match with the traditional one. I will check where does it come from.

The MC board model (Altium project) is attached as attachment 6. The schematic is attachment 5.