If you placed your waveport "inside" the radiation box, it would generate error message. A wave port MUST BE defined on the plane of the radiation boundary, not "inside" of radiation bounadary. That means, waveport and radiation plane must be on the same plane. IF you want to use wave port inside the radiation boundary, you have to use PEC cap on the back face of the wave port. The reason is PEC is non-solve-inside object, hence the face of the port touching PEC cap would not be solved inside by HFSS, but the other face of the port that touches your transmission line is then regarded as the excitation cross section.
Look at the figures below attached to know about the setup of PEC cap with an "internal waveport".