Wikitude's PhoneGap plugin is by design fullscreen. Once you call loadArchitectWorld() a fullscreen view is added to phoneGap activity's parent view that handles any "AR."-Components.
Best practice is therefore to define anything to AR inside the "Wikitude SDK html" and use the urlListener-concept (fires event in phonegap when you call "document.location = architectdk://..." in ARchitect World) to pass information between AR and PhoneGap, e.g. to exit AR view.
Please also have a look at the provided Samples in the Wikitude github account.
Kind regards