Updates:
We have managed to extract the recipient using extended properties and loading Internet message headers, but unfortunately this solution doesn't cover all the problems.
We have noticed that sometimes when we send emails from Outlook to an alias, and if we check the Sent items folder after sending, the recipient of the mail is changed to the primary address. In these cases, no matter how we try to extract the recipient of the incoming mail through EWS it will always contain the primary address. Is there a setting in Outlook or in Exchange Server that affects this? We've already tried the Automatic name checking and Auto complete settings, but without much success. Oddly enough, when using Outlook sometimes it changes the recipient, other times it doesn't. (When using OWA the email address is always replaced)
So the main question is whether e-mail aliases can be used reliably to distinguish incoming messages, and if so, could you provide guidance on how to do so?