I have an app in Windows Store and I've only targeted Windows Desktop because as per my knowledge, ARM config is for Windows Mobile, but my app cannot build packages for ARM due to some errors, so I've created my app bundle on x86 and x64 and uploaded the bundle to the store.
Now my question is should I make it available on Windows Mobile as well? because when VS runs the app on emulator (any CPU config) it builds it in x64 and then deploys to mobile emulator, why is that? Shouldn't it be building it in ARM config when trying to deploy on a mobile emulator?
ARM, x86, x64 are CPU architectures, different architectures support different instructions. Your source code is compiled down to CPU instructions, that's why you have to do it for each architecture once.
The mobile emulator still runs on the CPU of your PC, so it uses the x64 architecture. But this code will not work on your ARM phone, because its CPU simply cannot execute the compiled instructions.