For Lets Encrypt to issue and autoupdate certificates, the public_html/.well-known/acme-challenge/ directory MUST be accessible.
The Plugin does not support this. Most of the Panels does support Lets Encrypt nowadays.
https://www.virtualmin.com/node/41543#comment-760360
Please consider implementing the functionality.
https://wordpress.org/plugins/all-in-one-wp-security-and-firewall/