I don't know how it works for the digital versions, but with the physical copies the Collectors items are a separate code (literally a separate piece of a paper with a separate code, as well as the main game code).

Do you have to put in your Square Enix username at some point? I guess that when it does that it'll apply the standard or collectors edition to your account (if not, I fail to see how you can possibly get either version without an actual game code).

But I don't think you'll have any problems getting the collectors items, but buying the digital upgrade would have been cheaper!