It occurs to me I could structure my project to have my main node do nothing but free itself. I could have all the usual startup logic handled by an autoload instead. The benefit of doing it like this way would be to make this node, with all its crucial, top-level functionality, like swapping between scenes and so forth, globally available while keeping these functions centralized in one place.
It doesn't sound like the documentation intends for auto-loads to be used in this way. Is there a good reason why they shouldn't be? Likewise, what is the alternative? How is the functionality of the main node meant to be accessed by other nodes in the hierarchy?