The boundary conditions at the edges of the custom extent regions are taken from the boundary conditions on the wave port plane. The following image shows the real part of the electric field for a port with custom extents that's been applied to a metal trace.
In this image, no boundary condition has been explicitly applied to the port plane, so the default port plane boundary of PMC is used. It is clear from the image that the electric field vectors at the boundaries of the custom extents have no normal component to the boundary, indicating the presence of PMC in the mode solution. The only exception is the fields along the bottom boundary of the custom extent region, because of the presence of the PEC ground plane.
The next image shows the same geometry where a PEC impedance boundary condition has been applied to the port plane.
Now, the electric fields at the boundaries of the custom port extents have no tangential component, as we would expect for PEC boundaries.