My UWP app has two architecture configurations: "x86" and "ARM".
Until now (Win 8.1) the apps were built on the developer PCs and then uploaded to the store. Now, the apps are built "in the cloud" at Microsoft using .NET Native.
Can I be sure, that there (in the cloud) only x86 and ARM will be used to compile? (i.e. can I be sure that there will be no "x64"?)
They were always built on Microsoft machines, nothing very new under the sun. Prior to the .NET Native tool chain there was the MDIL precompiler, they didn't do a lot of bragging about it. The only reason you have .NET Native on your machine is to test your program. It is not very reliable with it being crummy at recognizing classes used in reflection code, you have to flush that out yourself.
You submit the MSIL assemblies, not the Native build, normally suitable to target any architecture. And sure, you specify what architectures you want to support when you submit your app. If you omit x64 then the Store machines won't try to build it and won't offer the download option.