If the custom extent of several wave ports touch or overlap, the resulting wave port plane extends over all connected sets of custom extents, and the port solve includes all involved wave ports. This is exactly what would happen if you hadn't used custom extents, except that the wave port plane is limited to the combined custom-extent region. The following image shows a geometry where the custom extent regions overlap.
The custom extent region is the union of the two sets of custom extents. The next figure shows the port mesh, so that you can see the combined custom extent region.
There is little reason to use custom extents in a system as simple as this one, but as before, this method is very useful in complex systems.