Hola
Sure - Dorito is a rig where you can control the deformed surface with controller, and transform the controller with same surface. In the example file you can see that mesh is deformed by morph but joints stay attached. Now, if you double click to select the joint and transform it the surface is deformed.
Second file is showcase of how to overcome dynamics limitation. Currently transformations made by dynamics are not recognized by effectors, so, for example if you want your clones to change color once they fall into certain area it simply won't work because as far as the cloner is concerned they haven't moved. In that scene I use inheritance effector to pass transformations and thus recognizing transforms
Hope this helps :)