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In my experience, as long as the address listed in the To: field survives the alias mapping/interpretation, you should be fine. Since Exchange does not preserve the original To: address when utilizing an alias, I typically recommend that you set up two mailboxes (one as the IMAP box that MP checks, and the other to forward jobs to the primary mailbox).
The first address/mailbox would be something like email@example.com with an alias of firstname.lastname@example.org. This results in being able to advertise the email address bwprints@mydomain (which is parallel in name to the one for color jobs) so that emails sent to the bwprints address are delivered to the mobileprint mailbox, and appearing to have been sent to email@example.com (which is defined as the primary email address in the MP web admin).
I then recommend setting up a second mailbox with an email address of firstname.lastname@example.org. It should be set to forward all mail to email@example.com. (If using PowerShell... Set-Mailbox -Identity colorprints -ForwardingAddress firstname.lastname@example.org -DeliverToMailboxAndForward $False).
The reason for the triple email addresses is that MP (at least 1.3.2) sends out the job status notifications and registration requests from the primary email address as defined in the we admin. This configuration allows the outgoing emails that students receive to originate from email@example.com instead of firstname.lastname@example.org which could be confusing if a student is printing a color job and receiving a confirmation from bwprints. The mail forward on colorprint allows emails sent to colorprints to be delivered to the mobileprint mailbox while preserving the original destination in the To: field, and setting the mailbox delivery option to false prevents the mailbox from filling up.
Edit: To answer your question more specifically, I have used both aliases and forwards. When Pharos checks the single IMAP mailbox for which it has been configured, the important thing is that MP is going to attempt to match up the To: address on each of the emails in the inbox to the various email addresses configured in the web admin in order to determine mono vs. color, and simplex vs. duplex. If the to address is modified - as Exchange does for aliases - the student is not going to get a print job that matches what they wanted. As long as the To: address is maintained (or the change is anticipated as with the Exchange configuration above), you should be fine regardless of wether you are using separate mailboxes with forwards, aliases, or any other configuration.
P.S. If you are not using exchange, just set up a single email address with a single alias for color jobs. I typically recommend a generic name so that outgoing emails do not generate confusion.
Your comment about how Exchange deals with alias had me experimenting. We have an Exchange server here and I frequently get email to one of several alias where the alias address is displayed in the "to" line. Looking into the behavior a bit more and it seams that what is displayed in the "to" line depends on what email client is being used to access the message. Microsoft's Exchange clients (Outlook 2010, 2011, 2013) replace the email alias with that of the primary address, whereas other mail clients may or may not do the same substitution.
Your suggestion would be the most straight forward method of making sure you get consistent results.
One other thing to consider is that if you are utilizing the upload feature, the uploaded jobs will default to the attributes assigned to the primary email address defined in the MP web admin. That would be a possible reason to flip-flop the color and mono email addresses. In MP 2.0 which released today, the expectation is that even if you disable the ability to release the print jobs from within My Print Center, users CAN use the document options buttons to modify the document properties for release via another release mechanism (Pharos Station, iMFP, Omega, Remote, and so forth). This is a huge improvement over 1.3.2 for those who do not wish to allow releasing jobs from the web page or from a cell phone, but still want users to have the ability to control what they get on the printer without having to upload a document 5 times (or forward it 5 times) just to get 5 copies, nor will they have to jump through hoops to keep or eliminate color from their jobs when uploading in MP 2.0.