I just want to confirm that even though your (NA) character isn't showing up on the Mog Station OR on the PS3 after you entered your code, you will still get your items from the Collector's edition!
・Helm of Light
・Baby Behemoth
・Behemoth Barding
・Coeurl Bell
After I entered my PS3 Collecter's Edition 12 digit code into PSN, I checked ACCOUNT MANAGEMENT--> TRANSACTION MANAGEMENT --> SERVICES LIST --> FINAL FANTASY XIV: A REALM REBORN.
It showed my subscribed services for the game.
FINAL FANTASY XIV: A Realm Reborn Collectors Editon Pack
FINAL FANTASY XIV: A Realm Reborn Early Access
FINAL FANTASY XIV: A Realm Reborn Open Beta
A quick note:(If you were prompted to download the game client on the PS3 but you already did during beta test or early access, you do not need to re-download the game client)
Then when I started up the game on PS3, I entered my password at the login screen and a terms of agreement appeared.
I carefully read what was displayed on screen and followed through without creating a new account.
A list then appeared showing what bonus items I was going to get.
On the list, it didn't show any of my (NA) characters I had made during beta. I was alarmed by this and was afraid to continue.
On the screen, it only displayed my character I had made in the (JP) server a while back.
I then went to the Mog Station website and checked if the list from the PS3 was the same.
It was the same on the PS3's screen.
I didn't see any of my (NA) characters on the Mog Station, only the (JP) character I made.
Taking a leap of faith, I went back to the PS3 and I clicked next to apply the benefits to my account.
Afterwards, I checked the Mog Station and all my (NA) characters appeared as well as my (JP) character.
(It also added 30 days to my subscription to play the game)
So in conclusion, it's safe to apply the collectors edition benefits to your account even though your (NA) characters aren't appearing on the Mog Station or the List on the PS3 that appears. Hope that helps!
Here is the photo for reference!