kupo and MK26, the distinction originally existed because we chose our first stage randomly. The idea is that there are certain stages which are just drastically terrible for some characters, like Brinstar, Rainbow Cruise, and Mute City, so those stages are going to be distinguished counterpicks. In other words, they cannot be chosen for the first match of the set (at least not randomly), because that would potentially screw over certain characters.
However, we started using that little strike system, which means that this is no longer a reasonable fear. You can now strike the stages that will screw you over, so the distinction feels a little antiquated to me. Personally, I don't see a point in it, and think we should only distinguish between "legal" and "banned" stages.