What is easier to do if you have 2 versions of 1 scene is just paste them after eachother in the same m2v stream and during authoring make 2 different chapter playlist, each with one version of the scene. GOPs have to be closed. I authored with dvd-lab and the point in the movie where a chapter will be skipped was marked as a layerbreak. The result is that a pause can be visible on some dvd players. I solved this by editing the ifo file with dvdremake and mark all chapter points as seamless. I've tried it once to make an edit of Star Wars with deleted scenes and it played seamless. Only thing is you can get trouble with the audio track. For example, in Ep. 4 the Death Star battle has changed quite a bit. Sometimes the sound of an explosion continues in the next scene. But in the SE that next scene can be very different with different audio so you won't get a smooth transition. A solution can be to take a large enough piece of footage so it starts with the same audio.
Combining scenes to make a branching version containing basically 5 movies seems too difficult for me with all the different audio and also colors/saturation/LD source. I think some scenes will stick out too much. Maybe a bracnhing version of the OT and the SE but that's it. More would be too complicated, for me anyway. AOTC and ROTS with the option "deleted scenes" is pretty easy to make.