Would it be possible for the Decker executable to look for a default .deck file on startup? So that way all you would have to do is throw the Decker .exe and the .dll files and a "main.deck" file into a folder, rename the executable and voila, it's basically the same as a native export. And if there's no "main.deck" in the same directory, it will just boot as normal.
One other issue along these lines I'd like to mention: If you open a protected deck and then try to close the application, it warns you about unsaved changes. I think for a protected deck it shouldn't warn you about that.