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I'm gonna multi post here, but whatever;
I have a theory on these questions but I'm too impatient to see other's thoughts on the subject. I think that the Dark Sign was placed on those who not only were useful to the gods but deemed dangerous due to this, but to those who are seen as a threat. In essence human warriors who achieved great power were cursed with the sign.
Why? Well if you recall, Humans who have their humanity drive them mad turn into the awful creatures, Manus included, we see in the Oolacile DLC in DaS1. It's my belief that the undead curse was developed in response to the Oolacile incident in order to manipulate and control humans they deemed too powerful appropriately. This is why so much emphasis is placed on the plundering of the grave of primeval man, they perturbed his grave and probably offered humanity to it.
In essence the Dark Sign is just a way to seal away mankind's raw power potential.
The reason why all humans who achieve enough power are seen as threats is because as the DLC in DaS3 confirms, man is in fact a direct descendant of the Furtive Pygmy, in fact after he, many followed suit. There was in fact multiple pygmy kings. Whether he created them or not, is a mystery, but from one many came. This doesn't explain however just what is the abyss, since even though Dragons can survive it as shown by Kalameet, it still doesn't explain why dragons can be corrupted by the Abyss after they consume it long enough. It still doesn't explain why humans can be corrupted by the abyss either.
Maybe the Abyss is just a side effect of the flame and the TRUE equilibrium state is the primordial, boring, grey land full of Everlasting Dragons, and clams. Regardless one thing has not changed humanity is fucked unless they turn into Dragonoids, fuck over the gods and quarantine the Abyss.