It has been confirmed on Blu-ray.com that if you buy the BD and use the digital copy code for the iTunes version you get all the iTunes extras, including the enhanced commentary, as well. Still not as good as having it on the disc but, at least we'll have access to it. Also, the digital copy code works for both UV and iTunes and it let's you get both, no need to choose.
Also, iTunes extras can not be played on iPhones, iPads or iPods, it can only be played back through iTunes on a Mac or PC. If you have an AppleTV, you can use AirPlay to stream it from iTunes to your TV. This is the big down side to iTunes extras, you are very limited in how you can watch them.
I really want to know if there is a difference, and what that difference may be, between the exclusive extras from Best Buy and Target. I look forward to the TrekCore review, hope it is out before the actual release otherwise I will go with the Target version.