So I could just put values (like site-url*) into app.arc with default settings and reset them from news.arc. Provided that it's utilized dynamically then all is good.
However lacking this functionality in arc I would just move the required config settings to app.arc and be done with it. You're still loading app.arc at the top of news.arc so the only real problem is app users need to know to change the settings therein (a comment would do).