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.
To add: a lot of cert providers also offer ACME so while the primary user of ACME is LetsEncrypt, you can use the same tech and validations as LetsEncrypt on other vendors too.