Hello Hash,
the point is that you cannot define an unambigous impedance for waveguides with non-TEM modes. The voltage and current depend on the integration paths you choose. An unambigous definition is the one for the field impedance which is the relation of the fields Ex/Hy. You also get the same value if you use so-called generalized voltages and currents for which the E^2 and H^2 field is normalized to 1 integrating over the cross section (see Marcuvitz, Waveguide Handbook).
The important thing is: Everything works well, as long as you always use the same impedance definition in your circuits. The reason is that only the relation of impedances Z1/Z2 matters and not their absolute value.
Regards, gsassle