We are also dealing with this issue here and are wondering if anyone was able to resolve this.
On Live, we relied heavily on populating ExtensionCustomAttribute1 via Powershell (as we were directed by Microsoft), but now that DirSync is enabled on our mailbox objects we are no longer able to do so.
The operation on mailbox "Test User" failed because it's out of the current user's write scope. The action 'Set-Mailbox', 'ExtensionCustomAttribute1', can't be performed on the object 'Test User' because the object is being synchronized from your on-premises organization. This action should be performed on the object in your on-premises organization.
We were also able to get attribute values to flow successfully to the FIM Metaverse but they never reach the cloud or populate ExtensionCustomAttribute1, leaving us unable to modify this attribute in DirSync *or* Powershell.