Dave, the two mistakes and you're dead rule applies comprehensively. Scorpion is limited when starting a combo on the ground. Basically when you look at his 51% counter, that is only usable vs punishable moves, and very well timed jump ins. I have gotten Jax players with aaHPHP JK, teleport punch as Human Smoke on a simple jump in counter, but this is a very special case.
When looking at the actual mistakes, as in close kombat situations, landing into harpoons, etc, Human Smoke can still beat anyone with two combos where Scorpion would need 4 or 5. Getting caught in a punishment mode situation is something that rarely applies to the best of the best. Something that bothers me about Kaillera players is the number of times someone who thinks they are God does a punishable attack, and then doesn't get punished due to lag. It's terrible.
Basically I don't apply punishment mode situations to it because it's a different kind of mistake. If that were the case, Mileena would "Two mistakes and you're dead" vs several characters because she has a 50% counter, so does Kitana and moreso, and then Ermac and Sindel are more like 1 mistake and some chip damage and you're dead.
Basically, the most crucial mistakes in high level play are made in close range, which is a big part of the reason why Kabal, Human Smoke and Nightwolf are so effective.