You can stick multiple arches in the same binary, much like OSX does. I think you can have ARM, PowerPC, and x86 in the same executable, each with 32-bit and 64-bit varieties.
The way I understood it, Windows 10 universal apps are truly universal; if your device runs Windows 10, it runs the app. This can be achieved as duaneb said, using the same method Apple has been using since the Intel switch 10 years ago.