Not necessarily: if the PML is far away, it means the simulation region is large which impacts the memory requirements and simulation time. That said, the PML should be "far enough" so it doesn't affect the evanescent fields at the surface of the structure. Typically, a distance of half the maximum wavelength is usually enough, but some convergence testing will validate this.
Again, whether the structure should extend through the PML depends on what you are trying to model and is not limited to the PML in the z direction (it also depend on the propagation direction).
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New Post - Reply To: Extend structure through PML boundary in z direction
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