Webmail uses hostname certificate instead of the domain's certificate.

Symptoms

Accessing webmail via https://mail.mydomain.com generates an SSL error because the hostname SSL is used.

Description 

The SNI (Server Name Indication) configuration for a domain is not added until it is needed. So this SSL mismatch will occur if the domain does not have any emails added yet. 

Workaround

Add an email account under the domain in the following location of cPanel.

Home > Email > Email Accounts