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NPM also lets you use your own certificates. Pick the "Custom" option after you click "Add SSL certificate".
If your services are not public-facing and you can't use the HTTP challenge you have the alternative to use a real domain name and to ask the bot to verify access to your DNS service through an API token. In NPM it's called "DNS challenge" in the certificate options.
So instead of using something like "service.local" as the domain you would use "service.local.realdomain.tld", give the Let's Encrypt bot a token to the DNS service that you use to manage realdomain.tld, and ask for a wildcard cert for *.local.realdomain.tld.
Of course you will also need *.local.realdomain.tld to resolve to your server's private LAN IP. Typically people prefer do this in their LAN DNS but if it doesn't support that you can do it in the public DNS.