Okay, so yesterday I was able to get on to live chat and have to "code registered to wrong service account" issue escalated. But I get an email this morning saying

We are sorry that you are unable to register FINAL FANTASY XIV: A Real Reborn on your service account FFXIV 1.

Please note that we unfortunately cannot add a Windows registration code for FFXIV: ARR on your existing FFXIV (Version 1.0) Windows account.

A FFXIV: ARR PlayStation 3 and PC registration codes however can be applied to the same service account. For registration of a PS3 version you will need a PS3 (once). Each time you register a new platform (PlayStation 3 or Windows) to a service account you are granted 30 days free playtime.
Players with accounts from Final Fantasy XIV 1.0 will be able to play for free for the first 14 days following the launch of A Realm Reborn.


Please note that registration of FINAL FANTASY XIV: A Real Reborn directly on https://secure.square-enix.com will become possible closer to the release date of FINAL FANTASY XIV: A Real Reborn which is August 27th 2013.
WTF? I thought 1.0 was suppose to be fully compatible with 2.0? Not to mention the account I'm trying to merge to is a FF14 2.0 beta account, not a 1.0 account. The agent I talked to also didn't mention anything about this being a problem.