As you may be aware, currently Lync features need to be manually enabled (WI) after the user object has been created.
This is by design. An enhancement request (TF00700152) has been created detailing the feature: automate the process of Lync object creation.
The product team will evaluate the request and this feature may become available on a future release of the product.
Please refer to this article for updates or contact support referencing the Enhancement Request ID: TF00700152.