For instance how can I use my *.domain.com SSL certs and NPM to route containers to a subdomain without exposing them? The main domain is exposed.
You can use the DNS verification method. Either using nsupdate with bind or what ever protocol your DNS provider and favorite ACME (certbot, acme, lego, etc) utility supports. As long as your DNS server is publically reachable that will work, even if the subdomain itself doesn’t exist publically.
This is what I do as well. I have a public DNS record for my internal reverse proxy IP (no need to expose my public IP and associate it with my domain). I let NPM reach out to the DNS provider to complete verification challenge using an account token, NPM can then get a valid cert from Let’s Encrypt and nothing is exposed. All inbound traffic on 80/443 remains blocked as normal.
I don’t really understand what you’re getting at. The answer to OPs question is to use letsencrypt like everyone else.
They literally didn’t mention LE at all.
SSL is not LetsEncrypt, if you didn’t know.
