Steps to reproduce:
1. Open the attached project
2. Switch platform to Windows Store
3. Open the test.unity scene
4. Click on "File" -> "Build Settings"
5. Click on "Player Settings"
6. In the Inspector click on "Publishing Settings". You will find Publishing Settings -> Packaging -> Version. Observe, version is 2.2.0.0
7. Play the scene
8. Console prints 6.0 (Which is Windows Standalone Version under
Standalone -> Other Settings -> Mac App Store Options -> Version)

Note:
Some behavior with the UWP builds

Expected results: Calling Application.version from the Editor on UWP platform should return Version under UWP -> Publishing Settings -> Packaging -> Version
Actual results: Calling Application.version from the Editor on UWP platform returns the Windows Standalone Version under
Standalone -> Other Settings -> Mac App Store Options -> Version

Reproduced with: 2017.1.3p3, 2017.2.2p3, 2017.4.1f1, 2018.2.0a7, 2018.2.0a8

This is intended functionality; the UWP version can be read through WinRT API calls:

#if ENABLE_WINMD_SUPPORT
var ver = Windows.ApplicationModel.Package.Current.Id.Version;
Debug.Log(string.Format("{0}.{1}.{2}.{3}", ver.Major, ver.Minor, ver.Revision, ver.Build));
#endif