We would like to propose to include official port configuration options during the ArcGIS portal installation process to avoid clashes with other services. In larger IT infrastructures it's not feasible for individual services to insist on specific port numbers. We're also in the unfortunate position that the chosen port numbers collide with RPC ports that are default to an entire network across multiple sites and that we are not allowed to change at this point.
We are aware that we can configure those ports manually by modifying the server.xml file but are actively discouraged to do so by ESRI support since it would pose a violation of our support contract. Furthermore we are reluctant to do so because it's impossible for us to estimate the implications for internal calls in the current release.