I haven't tried with spark-submit, but in my notebooks I use the Filestore for this.

val fileConfig = ConfigFactory.parseFile(

  new File("/dbfs/FileStore/NotebookConfig/app.conf"))

(this is Typesafe)

You could also add the conf file as internal resource and pack it with the jar.

But of course only interesting if the conf file does not change a lot, otherwise you would need to build new jars for every change.