Hi,
I think that it is not working because from BP point those are different types of applications (when you launch it via browser it is considered as Browser-based app while from Desktop as Windows App).
Cannot test it but I believe that it will work with 2 Objects > 1st will navigate you through browser and launch the app, 2nd will attach that app to itself (it will need some experimenting, dunno if 2nd should be windows/browser app and you'll probably need to keep all App Modeler parameters empty and attach (and set parameters) with Navigate stage).