nautilus-application: Fix commit 2780ce87

In commit 2780ce87 we restored the --new-window option, but at
the same time we were creating a new window for any glib option like
gapplication-service.

Instead of that, check for known application options, and if not found
any, let gapplication manage them.

https://bugzilla.gnome.org/show_bug.cgi?id=738430