@lukelarris What you propose is definitely possible. We just haven't tried it.
In app.js, we listen for a passed-in argument called config
By default, it looks for a config.json present in the root directory
If you ran NodeBB with ./nodebb start --config="/relative/or/absolute/path/to/another/config", it should correctly start NodeBB using the second config file.
I don't know what would happen if you pointed --config to a non-existant file -- would NodeBB run through the setup script and save the new config? Beats me.