A cpanel instance can service only one domain. When you 'add' another domain, it is not really added but redirected to point to a subdomain of the main domain. The webserver is doing this redirection invisibly for the browser / spider so to them the second domain is an independent entity and not some subdomain. The redirection is not a 301, 302, 3548764 etc, but an internal instruction.
For example if you have the domain aaa.com and want to add the domain bbb.com, a subdomain bbb.aaa.com is createdm as you've noticed.
Whenever bbb.com is requested, Apache (the webserver) silently shows bbb.aaa.com instead. This silent redirection never gets detected by the web browser / spider. The trick is used to allow multiple domains with a single cpanel.
By manually pointing bbb.aaa.com to bbb.com you force a second redirection and it looks like this:
bbb.com -> (server redirection) -> bbb.aaa.com -> (your manual redirection) -> bbb.com -> (server redirection) -> bbb.aaa.com
The end result is the same and it won't affect your rankings
This could potentially be abused if you start linking your competitor's domain ddd.com to its corresponding subdomain ddd.ccc.com but no search engine with a half brain will ever consider such configuration as dupe content, nor will it split the link juice as it's a standard hack with cheap hosts.
Still, if your second domain is earning lots of money, it is better off with its own cpanel, aka another account. It adds costs but also improved security at the very least because it will be protected with different login data.