I think you may be misinformed. You can build an app and install it using VS. You don't even need VS, apps are just exe's in zip files. Compile and lay it out right and you're done. The Store isn't required to do any of that, so I don't know what the "UWP backend" is. You might look at Hockey app (pre acquisition) for evidence of an app distributor that wasn't Microsoft.
You compile it to each architecture before you send it to the Store. There's a compilation option to create a .appxbundle, which contains the bits for each arch. It's basically the same as iOS fat binaries.
