As far as I know, you can only register one e-mail address per account.
You can however, register multiple accounts with
According to the command line options, you can use
certbot register -m email@example.com to register a new account.
But as you might have guessed, you can only use one account (and thus one e-mail address) per certificate. If you need multiple certificates with each (or grouped) a different e-mail address, you can choose which account to use when requesting a new certificate.