You will need to build and publish all 3 packages. This is because of the native code that it is built on.
The user would not have to choose from different packages - the correct one is automatically downloaded from the store.
The store already handles all this just fine - it's quite common actually (there are lots of native libraries now like SQLite, Bing Maps etc that all uses C++ and thus can't run as AnyCPU). Even the Visual Studio tool for creating the packages can create all 3 in one go. So they made it really easy.
It isn't impossible to accomplish AnyCPU (although it would require code changes from us), but it would involve deploying all 3 binaries in the app (which are fairly large each), so you will essentially triple the app size that customers are downloading - just so you didn't have to upload 3 packages.
You could of course just upload the x86 package - it would then be downloaded on x64, and the app wouldn't be available on ARM devices.
