As you know, the phase is associated with a field component. So you can use the domiant field component. However, a better way might be to use S parameters. Eg in your case, you can use S21 to evaluate the phase. Onething you may need to consider is: where exactly do you want to quantify the phase? relative to source or any special location? the monitor gives the phase at the monitor plane, whether it is for field components or S parameters. You may need to remove the propagation phase from source to device front surface and the device back surface to the monitor, which has analytical solutions.
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