Steps to reproduce:
1. Build any project
2. Open visual studio solution
3. Tick Landscape and Landscape-flipped Supported orientations in Package.appxmanifest file
4. Deploy to Windows Phone 8.1 device. Application will still start as Portrait

Why is this issue not going to be fixed?
On Windows Phone (unlike Android), Start screen is always in portrait mode. When you start the application, the OS will first display the splash screen, and only then will read your preferences you specified in the application manifest. Since start screen is in portrait orientation, so will your app be at startup.

If you want to change the splashscreen to be landscape when the application starts, add a landscape splashscreen image.