What is Ethernet diff. pair referenced to between connector and magnetics
The whole point of using a differential pair for signalling is that there is no need for a reference plane to compute the odd mode (the signalling) impedance. When you do the calculation, there is an implicit reference plane mid-way between the two conductors. As the conductors are driven with opposing voltages, the voltage mid-way between them is always 0.
You can also define an even mode impedance, which is the same signal being carried on both conductors, and this is with respect to some remote reference plane. In the case of ethernet, this even mode signal is poorly driven and received, as it has to couple capacitively across the isolating magnetics at either end. This is the signal responsible for EMI via conducted emissions, so on many cables it's attenuated by lumps of ferrite on the cable that raise the even mode impedance further.