Okay, so I had a chance to check on this finally, so I thought I'd follow up.
The extra file does have everything you need in it. If you review the download list under Account Management - > Transaction Management, it does refer to it as the Pre Order Theme. However if you check your Services list which appears below the Download list under Transaction Management, you should see ARR listed. If you open it for more details, you'll see your Early Access code and your Standard Edition pack for pre-order items have already been registered.
Edited, Aug 15th 2013 12:39am by Xoie
Thanks for the follow-up, I appreciate it.
Sony's account management rivals Square's in terms of complexity. I don't see what you found. Maybe it's different by region (Canada here) but I don't see any Services list anywhere. I'm checking both the store and the account management websites and I looked everywhere I could on the PS3 itself yesterday. I see ARR in the transaction history, but not the theme. I see the theme in the download list, but there's no way to show details, it just takes me back to the game page on the store.
I'm not gonna worry too much about it anyway, I'll assume they know what they're doing