Please note that it is now possible to configure an alternate login ID (in some circumstances) for Skype for Business/Lync. This will most likely be of interest in cases where end users have email or SIP addresses that differ from their UPN and/or a UPN that is non-routable (jdoe@contoso.local).
You can read full requirements and other important technical details in the Windows IT Center.
Configuring Alternate Login ID
It was already possible for some time no? The docs website is date from February.
Jean-Philippe, the testing for the SfB portion was not finished and added to the document until recently.