Is it possible to install a separate SSL certificate for the 'www' alias?
There is no supported method for separating the "www" alias to another subdomain VirtualHost. Without the ability to separate the "www" alias, customized subdomains will continue to encounter conflicts with the main VirtualHost, as "www" would already exist in Apache's configuration.
It is possible to create a custom VirtualHost include to overwrite this, but this would not be compatible with AutoSSL. As this is the case, it would be best to ensure that any SSL Certificate that you are attempting to install includes the "www" alias.
We have further documentation on creating custom Apache Includes here: