The unlayered version was released the same day as they PDF, it wasn't a response to the questions about layers. Again, they key point here is that a document scan will automatically create layers, so that they exist is meaningless, and doesn't mean it was edited, other than by the computer interpreting it. See this description of how scanning works, or please, just try it yourself.
http://www.foxnews.com/politics/2011/04/29/expert-says-obamas-birth-certificate-legit/