Thank you for reaching to us and we appreciate your patience.
You can use wave port at the intended places even if that is not exterior to the substrate. You can define wave port intersecting with the substrate. Please make sure that you are defining a PEC backing to the wave port when it is interior to the model. If you are using the latest version of the software then this will be prompted with a window for specifying the same.
Best regards, Praneeth.
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