I believe intrinsic impedance is more tied to the medium, thus is defined in terms of magnetic and electric permeability and electrical conductivity, while characteristic impedance is a "wider" look at the impedance.
For example, you can calculate the intrinsic impedance of a 18 awg copper wire, or air, or a vacuum. If you wanted to use coax cable with an 18 awg core, you would be looking at the characteristic impedance, not the intrinsic impedance of the copper that will be carrying the waveform.
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