There are a few different basic 5x5's out there. Really the biggest points in them I got was, you are using the 3-5 biggest compound exercises that the body can handle the most bar weight and will give the most bang for one's buck.
I think one of Starr's reason for a clean, as it is still a pull but, it is more plyometric and explosive which most reg exercises are not. I also think it is a bit more technical to learn and a bit more advanced to do textbook with some good weight, so it should be done properly with light weights, until it is pretty much perfected and second nature IMO.
As far as deads!? It might depend on what you really want to do as it is just another of the larg(est) of the compound moves and can be more adaptable for someone built more for pulling ie: longer legs and arms perhaps.
The trap bar is also a very handy piece of equipment that trains the legs hips and back quite well.
I am more bias towards deads, because they have served me quite well over the years. High reps to singles, they are a great lift for me.
I think the biggest thing with 5x5's is to stay simple and put the hard work into a few big exercises, whilst adding weight and eating well.