In Unity 6 (and probably other versions)

When you have the Dedicated Server package (com.unity.dedicated-server) in your project, it's impossible to set the port by code.

transport.SetConnectionData(listen_address, port);

Will not work on the server. (I call this from inside a Start function, not awake)

I think this is wrong as scripts should have the "final word".

The Dedicated Server package (and the -port command line) should override Prefab/Inspector settings, but it should not override scripts if you have custom logic to determine the port and want to use Dedicated Server package for other things than determining the port.

In my opinion the priority for determining port should be
1 Scripts
2 -port command line
3 inspector settings

If a project wants to use the -port command, they will not set it by script, there is no reason to. But if a project wants to set it by script, its not possible right now if you need the dedicated server package for something else.

I have not tested it but it should be the same logic for the target framerate if you set it by code with Application.targetFrameRate it should have final authority.

At minimum the dedicated server package should have option to disable each CLI argument individually and they should all be unset by default, as this causes a lot of confusion why the scripts aren't working and those param aren't easy to find. It's a big problem right now for myTcg Engine asset on the unity store as it doesn't use this package but it gets added automatically for some users and they have no idea why the script to set port aren't working.