It's not an exact fit but I have a FC mate with a similar situation. She thought she bought the expansion while on the SE store account, but she must have accidentally bought as guest as she couldn't find the game on her order list. She got no e-mail about the code being available (neither did I, actually, though mine was there when I went into the Orders page)
I told her to locate the Pre-order confirmation email. At the bottom there is a link in a red box that says "Click here to get access to your products".
The title of the e-mail should be something like "Square Enix Pre-order confirmation".
Worked for her, so it's worth a shot?