I still cannot wrap my head around it, but it looks like both cables are doing the same.
Of course they do. It's just a mechanical reason that they look different. If you have a harddrive/CF solution which fits better into the case in the other direction you might prefer the other type of cable. It is very similar to SATA cables with angled connectors. You get them angled to the left or angled to the right. Depending on how the harddrive is mounted in the case you might need one or the other. And it is very disappointing if you bought the wrong one.
