angular.bootstrap() will throw an error if it is called twice. I don't think forcibly bootstrapping is the way to go here - it might not do what you want (what if your application needs to load modules with angular.bootstrap()? Protractor can't know what to do in that case).

I think the correct way to do this is that your test will have to figure out how to bootstrap, and then let Protractor know when your application is ready to begin testing. Before Angular is ready, you can interact via browser.driver (using webdriver directly).