As replied in your support ticket on the same matter:
"Unfortunately, it seems to me that Cordova for Windows Phone does not support the modifications necessary to get custom URI schemes to work out of the box. It is possible to add the necessary line in App.xaml.cs only when building a project through the Cordova command-line utility and only manually. It is not possible to do it using a plugin. It is also not possible to do it in the AppBuilder UI. In fact, for the Telerik Mobile Testing plugin we've added custom build steps to our Cordova build script that modify the App.xaml.cs file prior to compilation such that it can support something resembling custom URI schemes, to the extent allowed by the platform.
We could probably extend support for custom URI schemes in Windows Phone on our side. I suggest that you write a suggestion in our feedback portal regarding this.
As a workaround I can only suggest that you build the Windows Phone 8 application package locally using the Cordova command-line utility.
Please, feel free to contact us again if needed here, or in your support ticket.