Silo 2.0 has the resurface topology option, where you can definately edit every vertex and edge, even extrude, rotate, bridge, on top of the model as you retopologize it. The topology brush can also be used to combine it with the surface snapping. I checked out those videos myself on TopoGun, but i think silo has smarter tools still.
But i think this TopoGun tool, can be improved and it looks like its on a good path. It would be nice if you could use TopoGun to work like Maya and zbrush, where you can hit a button and it tries to get your low res model conform onto your hi-res model and to update the low res to make it look like the hi-res. Zack Patrock has a DVD like that. He uses a mel script in maya to do that.