Not sure I follow, we run nginx and certbot in Docker too? It's just that we manually manage its configuration, and need the extra (not too cumbersome) steps to get a cert up.

I usually copy a vhost config from one of our templates, comment out the TLS vhost, reload nginx, request cert, uncomment TLS vhost, reload nginx.

So, I'm not sure what's not possible in your setup? Unless there's a limitation on what kind of volumes you can connect to your containers?