Passenger is an application server that can either run as a plug-in to a web server, just like fastcgi or mod_php, or as a stand-alone server. When it runs as a stand-alone server, it actually uses an embedded copy of nginx as part of its code—but don't let that confuse you. It's still an application server, running as a separate process from the 'http' nginx server that is listening for requests from browsers. That 'http' server needs to be configured with a reverse proxy to the application server.
And an aside: Passenger is the best-documented, easiest to use application server I have ever used. I would not be so quick to run away from it. Figure out what your certbot issue is and fix that. You have a lot more work ahead of you to use a different approach.
Walter
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