Some cases don't really have a convenient sized pocket, especially with phase gear because you end up carrying 5 to 8 batteries. Using an extra space in between divisions in the bag itself probably won't keep them from slipping around and ending up somewhere else, so it might be more about keeping things organizing and not damaging things.
Personally I use one of those velcro bag things Phase ships some of their stuff in ... just a big flat thing that you fold the corners in on and make into a bag of various sizes. I folded it so it holds six batteries all side by side, tight enough they don't slip on top of each other. This lays neatly over one compartment in the bag, just the right size.