I have several customers in O365 that have their UPN and SMTP address different. This isn't a hard blocker, but you may see odd behavior for new users. i.e. If you use the Email attribute in AD to create users instead of ProxyAddresses, the SMTP
address in O365 will match the UPN.
UPN's in O365 (for transitioned accounts) should not be affected, but SMTP address can be affected since DirSync will make these changes upon initial sync to match what is in your on-premises AD.
For the first sync of DirSync v2, objects are matched based in this priority: Primary SMTP Address, Email Address, UPN. New users are created in the same manner, but, if there is no proxy address, it will be created based on the Email attribute, but
the primary SMTP address will be matched to the UPN (unlike BPOS which would just create a proxy address based on the Email attribute and ignore the UPN.
Glad I could toss more confusion on the fire.
Dan
www.insecurityinc.info