I've gone back to Atari's site and understand that the ship is not listed in the description.(curently)
Beleive me when I say that in January when I ordered it, Atari did indeed have it listed in the description, I compared it and the other 10 places to preoder and the bonuses that came with it. It was listed in the general discription and all the other extras where listed off below. I think who ever did the website info got mixed up on what they offerd and changed it later to reflect the proper info.
Be that as it may or may not be, it could be the reason for others having the same problem with their Atari preorder's by expecting things they thought were in the preorder.
The only solution is to overlook this rather I'm right or wrong and pick up another Digital key from a retailer and stack over the items I have to gain that ship.
Thanks guys, I hope this helps some other peoiple.
I myself bought the gamestop version specifically for the Connie. I never saw any other offers from any other companies that included a Constitution class. Not saying it didnt happen, just saying I never saw it, and I checked around (checked steam, amazon, atari etc ), since I generally prefer not to buy from Gamestop.
I wish cryptic and all involved would have made finding the bonus items a tad easier, and more intuitive. I dont look for my free bonus items in the store menu normally. Nor do i expect the bonus ship to end up in my inventory. (I looked at the shipyard selection menu first, and of course it was in my backpack)
Of course gamestop included absolutely no instructions with the download link (digital deluxe version). So no one had any idea unless you happened to go back the gamestop website and scroll down and notice they changed the advertisement to mention "look in the c-store". Bah.