Sorry to reply you late due to some circumstances.
Yo are right. In FDTD the simulated transmission or reflection is always normalized with the source spectrum, which is from the time-dependent signals. Once the result removes the source-dependency, you can multiply your source spectrum to get the absolute results. However, since most deivces work linearly, please make sure it is reasoable to use absolute value, as many experiments also give normalized results.
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