The 5" plate is better because the Propel pads have a depression in the back of the pad, which happens to be 5" in diameter. It's exactly the size of the 5" backing plate, which makes it very easy to center the pad every time.
I think the smaller backing plate would enable you to better access tight areas, because you can move the pad under a spoiler, for example. The larger the diameter of the backing plate, the less pad you can move under the spoiler without having the plate contact the spoiler. I think that made sense...