I believe this only applies to an iCloud account ID, where your @me, @mac or @icloud email address can be used interchangeably with your primary email address (ID) to sign into your iCloud account or other services.
As far as I know, there is still no way to merge different Apple IDs. You could contact iTunes store support with your example and ask them for clarification on this: http://www.apple.com/emea/support/itunes/contact.html.
When you create an AppleID with an existing mail address (let's say email@example.com) you have the option to, next to this, create an iCloud mail address (or, in the past a me.com mail address/mac.com mail address). You do this by going to iCloud on one of your devices and activating the mail tab. This will allow you to create such a mail address and this mail address is then linked to your account as both an active, working mail address and an AppleID alias that you can use to login to all of Apple's services.
This mail address, however, has to be new - it can't be existing - and it therefore can NOT be used to merge two accounts. Apple does not allow you to merge two accounts at this moment and it does not look like it will be allowing this in the future.