SPARK-2664. Deal with `--conf` options in spark-submit that relate to fl...

...ags
The spark.app.name already gets set above with:
      OptionAssigner(args.name, ALL_CLUSTER_MGRS, ALL_DEPLOY_MODES, sysProp = "spark.app.name"),
so this is just removing a redundancy.

For reasons that are too boring to be worth going into, this was more thematically affiliated to the rest of the changes before I rebased it.  Not strictly related to this patch anymore, so I can fix it separately if you'd like.