> we need to run application in "dev" mode but with the "staged" version
You could write a wrapper around play.core.server.DevServerStart and then override application entry point with the main option, e.g.: ./target/universal/stage/bin/my-application -main org.example.MyServerStart. That seems pretty pointless to me, however.
> because some debug instruction are only run on dev mode
There are exactly zero differences between prod and dev modes in that regard.