Although the previous Intel Atom architecture was only 32-bit and had some hard limitations baked in it, the new one supports both 32-bit and the 64-bit extensions, just like Intel’s other chips, although for the very first versions of this architecture, the 64-bit extension seems to have been disabled (probably to save cost, and because the OS wouldn’t need it at the time anyway).
Intel is now saying that they’ve already finished pushing the 64-bit optimizations for KitKat. Intel is the one making sure the latest versions of Android work on its chips, so now they’ve not only made sure KitKat works on its latest Atom chips, but also that the 64-bit extension works, so they probably had to modify that version of KitKat to support 64-bit.
Google doesn’t yet support 64-bit in Android, but hopefully with all latest craze about ARMv8 and 64-bit chips, they’re going to use a Linux kernel that fully supports ARMv8 in the next version of Android, whether it’s Android 4.5 or 5.0 (I’m hoping 5.0, so we can already see devices coming out with it at the end of the year). Obviously, support for 64-bit was already baked in the old Linux kernels.