I've finally gotten around to adding the preorder code to my account. Turns out instead of being a simple copy/paste job that you need to go to a second site to redeem the pre-order code in order to get the actual item code that you can copy/paste into your account page to redeem it.
I mean, they did ask me which version I wanted when I was ordering it, so it's not really as though going to a separate site to redeem the code was really required. They could have just e-mailed the code to me. Or even better, allowed you to preorder through the Mogstation and apply it automatically.
Though really, I don't know what I was expecting, Squenix don't have a good track record when it comes to make things simple for the end user.