I use LDAP for user store. I have set up "mail" and "otherMailbox" as threepid email attributes. When people get invited to rooms, they receive 2 (sometimes 3) invitation e-mails if they have the same e-mail address in LDAP "mail" and "otherMailbox" fields. I think it's a good idea to check identity store for duplicates before sending invitation e-mails.