Certbot is the new name for letsencrypt and it’s still possible to get a certificate covering multiple domains.
If you know at the outset what domains you want to be included in the certificate, it’s not necessary to edit any configuration files. Instead, you can specify the domains on the command line when you first run certbot. For example, you might run something like
certbot-auto -d one.example.com -d two.example.com -d three.example.com -d example.orgThis will request a certificate covering all of those names. When renewing the certificate with certbot-auto renew, it will be replaced with a new certificate that still covers all of the names.