And will the application only work on Windows systems on which the .NET Framework 4.6 is installed?
No, it works on any machine or device capable of running universal applications. The version number of the frame version disappears after the Store packs your application, the framework methods you use are compiled into the package. Run .NET Native, a time-ahead compiler for universal applications. The package even works on a device on which the .NET Framework is not installed, for example, on a phone.
Thus, the structure you choose does not matter. Choosing 4.5.1 or 4.5.2 or 4.6 does not give you additional options; in these runtime versions there were very few new api additions. But first of all, you build your project with the help of reference assemblies that do not reveal them. Notice how you can select 3.5 from the drop-down list, and that doesn't matter.
Project Overview> Properties> Application Tab. What is really important, you are targeting a universal version. For now, just create 10240 so you don't have to worry. The framework version, designed for purposes, is a subset of the .NET Framework that you have on your computer called .NETCore. This is much smaller than the full version.
Remember to check your Release build, which is very important for .NET Native.