I'm sure @bonienl will tell you that the UI is not looking at the template / configuration for the ports in use but rather it constructs it by inspecting the docker container itself for ports (ie docker inspect container). The official EmbyServer has this snippet
"ExposedPorts": {
"1900/udp": {},
"7359/udp": {},
"8096/tcp": {},
"8920/tcp": {}
},
Also, you need to understand that once the container get its own custom IP address, all the port mappings are ignored, so your unRAID port 80 and nginx port 80 are not in conflict, particularly since the host can't use the custom IP of the container and vice versa. Its like when you run multiple VMs, each with its own IP running a webserver on port 80. To migrate, say emby, to use port 80, you'll need to change the port setting in the server dashboard, and not on the container settings from unRAID UI
Hope this make it clear.