The only thing it will install is docker.
Looks good.
app.yml gets created by discourse-setup. You can’t run discourse-setup if it can’t access the ports, but if you read the source you’ll see that you can ./discourse-setup --skip-connection-test and run it anyway.
Your nginx will be responsible for let’s encrypt, so you’ll want to comment out the let’s encrypt template. I suspect that’s described in the reverse proxy topic linked above and below.
See Using Nginx Proxy Manager to manage multiple sites with Discourse or Run other websites on the same machine as Discourse (which has already been linked).