WHM/cPanel

here is the solution. It is not ideal bot it looks like there's not much we can do, having cPanel/WHM installed.

<VirtualHost x.x.x.x:443>
    ServerName domain.net
    ServerAlias www.domain.net
    DocumentRoot /home/user/public_html
    #todo common contact mail
    ServerAdmin support@domain.net
    UseCanonicalName Off
    <IfModule mod_suphp.c>
        suPHP_UserGroup user user
    </IfModule>
    <IfModule ssl_module>
        SSLEngine on
        SSLCertificateFile /etc/letsencrypt/live/domain.net/cert.pem
        SSLCertificateKeyFile /etc/letsencrypt/live/domain.net/privkey.pem
        SSLCertificateChainFile /etc/letsencrypt/live/domain.net/chain.pem
        SetEnvIf User-Agent ".*MSIE.*" nokeepalive ssl-unclean-shutdown
    </IfModule>
    <IfModule headers_module>
        RequestHeader set X-HTTPS 1
    </IfModule>
</VirtualHost>

• redirect from 80 to 443 set separately:

    
    RewriteEngine On 
    RewriteRule ^/?(.*) https://%{SERVER_NAME}/$1 [R,L]