The advantage of mixing your materials via nodes is that you are not limited to 2 materials. Let me explain what I mean. With nodes you can mix as much materials you want together, and always put the new textures on top of everything. The Problem with stencils in the textureslot is that every new stencillayer you use is affected by the stenicillayer above. If you are using only two different materials it is no problem. As far as you start mixing 3 different diffusetextures you will have a problem, that you are not able to put the each new texture just on top of everything. I hope you understand what I mean.
Unfortunately there is a bug at the moment. The bge doesn’t use the right UVLayout. In the Viewport everthing looks ok, but as far as you start the bge it uses the UVLayout that is selected in the Object data and not in the in the nodes. I’ve already reported that bug and it has been confirmed. So I think the fix will be soon in trunk.