One of the problems is that LetsEncrypt currently requires the web server making the request to be on the standard HTTP port 80 and HTTPS port 443. By default VPOP3 uses an alternative port so that it does not conflict with any other HTTP or HTTPS server on the same IP address.
So, we can't use LetsEncrypt without having VPOP3 use ports 80 and 443 which would preclude the use of any other web server on the same IP address. This would lead to lots of support issues...
https://community.letsencrypt.org/t/support-for-ports-other-than-80-and-443/3419/100