WHM and cPanel run separately from the webserver and have their own self signed certificate issued by the server this allows secure access to whm on port 2087 and to cpanel on port 2083. This is installed as part of the setup of the server and is issued to the server name, it can not be used for other domains or accounts.
SSL for your domain runs on the webserver and allows access on port 443 this is completely separate from WHM/cPanel access.
SSL for your domain runs on the webserver and allows access on port 443 this is completely separate from WHM/cPanel access.
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