So this is my situation.
Back during Final Fantasy XI I made an account on the NA servers.

I pre-ordered a boxed Collectors Edition from EB Games in Australia which is EU region.
Received the physical copy early yesterday and tried to register it. Only to get told that my code was invalid because my account must be in the same region.

Now when I received my pre-order code it said "If you do NOT have an EXISTING account". Nothing about if you do not have an EU account. When I input my pre-order code there was no message that said your pre-order code is in the wrong region, please make a new account.
Instead it took my pre-order code, allowed me to redeem it, but did not send a 20 digit windows code. I could go to my account and see that FFXIV:ARR had been added, but it didn't have early access. In the end a friend gave me an unused pre-order code he had which worked so I got Early Access (due to finish in 2 days).

Regarding my physical copy, I contact Support to ask to get my account transferred to EU. Nope, cannot do...they don't do region transfers.

Their solution:
Make a new EU account, lose my pre-order bonus, and my characters. And not be able to make a new character on Diablos with my son, my partner and a long standing linkshell.

or

Buy a NA collectors edition digital version, and apply it to my account which will cost me another $50USD. Only issue here is they have stopped sales on the download version through Square Enix, and Amazon does not sell outside NA.