Currently, the core bootstraps on initialization, usually when the graph or config API is first touched and CDI instantiates.

I think this is not much transparent - all the scanning of the addons, models, configuration is done in different call stacks, making debugging the bootstrapping difficult.

Better to have a special config and bootstrap aside.
Something along the lines of:

WindupEngine we = WindupEngine.create();
we.configure( new Configuration() );
we.run();

For standard CLI, it could go like:

public void main(String[] args) {
     furnace.getService().get(WindupProcessor.class)
       .init(WindupConfiguration.build(…)).process() ....
}

See: http://forge.jboss.org/document/run-forge-embedded