Your purpose is to " Transmission spectrum of light exiting through a metasurface", so it will depend on how do you define the metasurface.
The suggestion to include only a small portion of the substrate is to resolve the issue you experienced with no time signal in the time monitor, far below the nano-structure.
Since the substrate is in a few source wavelengths, and it is suspended in air, you should include it to get the transmission, with much longer simulation time and smaller autoshutoff min. You will need to let the back-and-forth reflections from the substrate decay completely in order to get the accurate result.
Please do not place the frequency-domain monitor exactly on the material surface.
I guess you have noticed that the second simulation takes longer time compared to the 1st one.
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