AutoSSL not applying to addon domains

Hello Everyone, I am using google cloud as hosting and i have installed cpanel on it. We are a a blogging platform and we provide free subdomains to user. We have purchased SSL certificate comodo from the SSL/Wizard in cpanel. This SSL certificate securing my main domain and their wildcard subdomains automatically. Now here comes a feature in which we provide custom domain to user if he wants to upgrade from the subdomain to own custom domain. It is all working with the help of Cpanel Addon Domains. So We point custom domain to the directory of subdomain that works perfect but now here comes the issue with SSL certificate which does not apply on the custom domain. As discussed with one member of Cpanel suggested us to use AutoSSL feature of cpanel which will solve our problem but unfortunately that didn't work for us. Below is the log file generated: The system queried for a temporary file at "http://domain.com/.well-known/pki-validation/18E1324AB139465868E2140514105BBA.txt", but the web server responded with the following error: 404 (Not Found). A DNS (Domain Name System) or web server misconfiguration may exist.
Some of geeks suggested to change .htaccess file as there could some redirection that creating the cause but We tried with the htaccess and removed https force redirection but again that not worked for us. So if anyone have a better and working solution then please help us. looking forward to see your response,thanks.