I'm sure there must be more deleted scenes. At the very least, there was an alternate scene between Kirk and Pike (we've seen stills of it, where they are both dressed in the grey uniforms and seated opposite each other) -- I think that was an early version of the bar scene. And I have no doubt there are more.
Maybe this is a "double dip" situation. A minimal-frills DVD/BD in September to cut down on piracy, and then a "special edition" version loaded with frills just in time for Christmas. Paramount wants to get more of my monies.