Create 2 surfaces:
1) The first by doing a copy-surface of the wetted surfaces inside the port.
2) The second just a flat surface at the station you want to measure the flow area at.
3) Trim the 2nd surface (use-quilt option) with the first surface.
The area of the final, trimmed surface will give you the physical flow area.
NB If there are a lot of small surfaces inside the port you may want to use the surface and bound option in copying surfaces.