It certainly seems from reading the above that Jesse was, in 2001 at least, advocating putting the entire codebase, or nearly so, for an application in a single file.
He's arguing for putting all of the controller code for one application into a single file. I can't see anything to disagree with about that. He doesn't say "jam all of your applications for a whole site into one file" nor does he say "put all the database code and templates into one file." I understand what you're objecting to, but it isn't a view supported by Jesse or any of the current CGI::Application developers.