You could use this guide, but change the DigiCert-parts with their Let’s Encrypt equivalents: https://www.digicert.com/ssl-certificate-installation-webmin.htm
Apparently, Webmin sucks and needs weird methods to work with an intermediate certificate.
You could try to concatenate privkey.pem and cert.pem to a single file and use that file as the “Private key file” in Webmin and add chain.pem to that other option? I dunno, but it’s worth a try 