In HFSS, for the waveport, the energy is fed to the system (or antenna) from outside, so the waveport must be placed at the outer boundary of the simulations box.
For the waveguide (or waveguide feed horn antenna) case, if you set up the waveport at the end of the waveguide, the feeding source is the intrinsic mode of the waveguide, for example, TE10 mode for the rectangular waveguide above its cut-off frequency. So this represents the idea case for waveguide fed antenna.
If you are also considering the coax-waveguide transits, you need to set up the waveport at the end of the coax-cable, and build your coax-waveguide transits by yourself. In this case, the structure will also include the transition loss or other issue associated with the structure.