According to http://doc.qt.io/qt-5/qmake-variable-reference.html#winrt-manifest it should be possible to override a list of application icons. While it seems to work with logo_store and logo_large, it fails with splash_screen and logo_small.
How it fails: The resulting packagage always contains the logo_44x44.png and logo_480x800.png from the Qt mkspecs directory. The app shows the Qt spash screen and ends up with the (blurry!) Qt logo in the application list.