I wanted to share that I encountered this issue too when trying to change the e-mail address of my Apple ID to another e-mail address. Even though I was using this address as an alternate contact address in FaceTime and iMessage, the system told me that it was used by another account. I found the activation e-mails from 3 years ago that I ignored at the time.
Obviously I wasn't able to access the account as I did not have the answers to the security questions. I was able to change the password and gather some information about it though.
In the end, I spoke with a very nice AppleCare senior advisor who wasn't able to gain access to the rogue account, but escalated the matter to engineering. In the end, they sent me a "Email Ownership Verification Code" to the e-mail address I wanted to use with a PIN. Gave the PIN to the senior advisor who sent it back to engineering. On the next day, my e-mail address was removed from the rogue account and became available again for me to use with my Apple ID.
Oubviously, the Apple system has some flaws:
- It likely shouldn't ask for security questions before you click on the e-mail validation link. That way, an e-mail address wouldn't be locked to a rogue account like that.
- It also shouldn't let you create an Apple ID with an e-mail address that is already in use with FaceTime and iMessage.
I hope this answer can help other people in the future.
Cheers!