Your Apple ID iCloud and Alias
After trying to find out how to lose the iCloud email associated with my Apple ID, and the confusion relating to the alias's that apple keep referring to in their articles, I think this is how it must work.
When you first set up your Apple ID you also set up an iCloud account. This account can have the same id as your Apple ID if your Apple ID ends with @icloud. If you choose to use another email address as your Apple ID, such as a Gmail email, then you must set up iCloud with an @icloud address. This address is then referred to as your Apple ID alias. As you can sign into your accounts with both id's.
If you don't want to use this @icloud address, you must turn it off in mail preferences. It cannot be deleted as it is directly linked to your Apple ID. You can make alias's of your @icloud address if you want more email addresses, or want to hide your original @icloud address but these alias's will not allow you to sign in to your apple devices.