

This is more than temporary the Lazarus Pit under Gotham City has apparently been destroyed, and with it goes the ultimate source for almost all the extra-normal aspects of this universe. The only remaining villains are people like Victor Zsasz and the Calendar Man - small-scale psychopaths without the desire or resources to plague the city in the way the supervillains or even the mobs did. Without their resources, their ability to be any sort of threat, in jail or not, is effectively eliminated. Not to mention they are stated to have pooled all their money into this one final attempt at beating Batman.
By the time of the Golden Ending, every single one of the major villains in the entire franchise are either locked up or dead, minimizing the chances of any future break-outs or team-ups (the latter didn't matter much anyway - the Villain Team-Up that received so much attention in the advertising was largely abandoned).

When all of this is considered, that he appears to have died and come back, doesn't that remind you of a certain someone.? Looking at the Scarecrow proves this, with his deformed face, his staggering walk, his barely-visible body, he genuinely looks like a person who died, rotted in the ground for a few months, and then suddenly started moving again. It was said somewhere that the concept behind the Scarecrow's new look in Arkham Knight stemmed from the idea of a living corpse, someone who had died and come back to life, but in the time between had rotted and decayed.
