I was also struggling to get Lets Encrypt Auto SSL for server hostname and CWP.admin and CWP.user panel. Today I am able to successfully make it. Hope AutoSSL renewal will happen by the end of current expiry date of the certificate.
Step 1: Create a subdomain as same as the server hostname ( For eg: if your vps server name is "server1" and main domain is "xyz.com" Subdomain and hostname should be "server1.xyz.com"
Step 2: If you check in the "List DNS Zones" under DNS Function menu, you can see a new zone created "server1.xyz.com.db" Click on "Edit Record" Blue button under the same zone, look for www record as below
www CNAME 14400 server1.xyz.com
Delete this entry and add an A record as below
www A 14400 ### Your Server Public IP ####
Step 3: If your DNS Manager is outside of the control panel. Some use FreeDNS Manager from Centos WebPanel or other third party DNS manager, make sure you add below A records
server1.xyz.com A 14400 ### Your Server Public IP ####
www.server1.xyz.com A 14400 ### Your Server Public IP ####
Step 4: Wait for at least 24 hours to propagate the DNS changes/updates
Step 5: After the DNS is propagated, Go to SSL Certificates Menu, Go to "AutoSSL [Free]" tab and select your user and under domain select the subdomain "server1.xyz.com" and click on Install SSL. If SSL installed successfully, you will get green popup message on the right corner of the webpage. If you are getting and DNS error message, wait for sometime to propagate DNS entries.(Some DNS requires 24 to 48 hours to propagate)
Step 6: If Step 5 is successful, Go to Installed SSL List and check Lets Encrypt certificate is installed or not for the subdomain "server1.xyz.com" with a validity of 89 days left.
Step 7: If you pass Step 6, Go to CWP.admin Dashboard and click edit button next to the hostname and open the "Change Hostname" page. Even though you are not changing the hostname which is set as "server1.xyz.com" before. Click on Change Hostname button on the bottom of the page. Wait for the successfull message on the top of the page. New SSL Certificate from Lets Encrypt should be there after you refresh you webpage or clear cache in browsers.
Step 8: Enjoy new CWP.admin control panel with any certificate warning message.
Now when I look into the installed certificate List, I see the subdomain certificate is showing "NOT INSTALLED". Hope this won't be an issue after 89days for auto renewal.