Ya, 4.6 has support for 64-bit in both shipping and development if you sync from GitHub yourself and shipping only if you use the binary release of the engine. You can specify the supported platforms in the Project Settings under the iOS section.
Yes, the currently available Tappy Chicken was built against 4.6 and has both a 32 bit and 64 bit version (as well as a Metal and a ES2 version). I have not yet uploaded the 4.7 version of Tappy Chicken to iTunes Connect as of yet, but I will update when I have.
We did discover a bug when updating the code signing for UDK and the fix for that was migrated over to 4.7. However, we didn’t ever see the same bug in UE4, so it was pulled over as a precautionary measure.
That is the exact bug that we found in the UDK version of the fat binary signing tools. The fix for that was added to 4.7 release. Try the 4.7 preview 6 release if you can. The 4.7 preview 5 was all sorts of incorrect because a number of fixes for iOS were merged right after it was pushed in to the release pipeline. Also, you could get around this by utilizing the 4.6.1 Mac editor to do the packaging. It does not have the signing error.
Where should I start looking in backporting the 64-bit support to 4.5.1? Apple started rejecting our pre-release builds today, one week before we have to leave for GDC. We thought pre-release builds classified for the June deadline since we uploaded several after the February 1st deadline, but seems it was a trap.
There’s no way we can port the game to 4.6 in such short notice (after failing twice) and 4.7 is still not stable enough (and I don’t know how much we’ll have to refactor to get around the inevitable unknown issues), so hacking 64-bit support into 4.5.1 is the only viable option right now.