On my end Jooby 4.0.10 still seems to ignore my application.conf server.port.

server {
port = 6001
port = ${?SERVER_PORT}

compressionLevel = 6
compressionLevel = ${?SERVER_COMPRESSION_LEVEL}
}

listening on:
http://localhost:8080/

on 4.0.7

listening on:
http://localhost:6001/