They are arranged with the smallest border necessary for performance reasons, but keeping eventual paperdoll spaces in mind (e.g. helmets, spears or other things which would go over the frame).
The bigger the dead space, the more performance / 2D memory on the graphic chip it usually costs, and it can quickly sum up if you are not using a sprite atlas system or texture packer. I can't really save the assets the right way for every project, because the animations needed and the way of implementation always differs, but FYI I was following the most common approach gamemaker / unity tutorials show.