I was reading the description here about having to pre-order the game to get the extras, but before that I checked my gaming sites like gamespot and gametrailers and their news said its not a preorder, its just an initial batch of launch copies that you need to buy while supplies last. There is no need to preorder.
Yes, all initial copies of Shift, regardless of the retailer, will be the "Limited Edition". EA has been doing this with a number of releases in the recent past. To name a few off the top of my head, Battlefield Bad Company 2, Medal of Honor, Need for Speed Hot Pursuit, Crysis 2, Bulletstorm, Battlefield 3.
How long these copies remain on store shelves depends on how large of a batch the publisher initially puts the "Limited" banner on, and how the game is selling.