The reason we only allow one domain is for security and performace. We use CageFS from CloudLinux which is a virtualized file system and a set of tools to contain each user in their own 'cage'. This prevents users on the server from being able to access other users files. With CageFS believe in only having one website per install. Real life Example, lets say you were hosting five client websites and an attacker was able to access one of the sites from an exploited plugin or update. Once they have access to the one site they may be able to have access to the other sites within your CPanel account. If you have everyone within their own Cpanel install that would not happen.
With performace each CPanel account has their allocated resources. If you have five websites within the same account they are all sharing the same resources.
This is why we suggest anyone that is hosting clients websites to sign up for our reseller plans which allows you to setup your clients within their own CPanel accounts.