The new instantMini version, build on OpenGL ES directly and not WebGL, provides an WebKit layer which supports x3dom content. It was tricky to get everything through the stringByEvaluatingJavaScriptFromString method but finally it works.
The current App does not just support X3D elements in the DOM but also additional elements to configure the vision subsystem (e.g. Marker). This system will also be shown on the Web3D booth (#1024) at siggraph next week