That thing the Joker bought from Riddler was the same liquid that made Joker
- In this case, the person Joker was threatening to kill would be Harvey Dent, leaving nothing but a psychopath like Harvey's worse half in control.
The Riddler sold the Joker stolen technology for making artificial life
- The Joker had figured out a way to use this technology to kill Harvey's worse half. The reason Two-Face knows a man that can "make everything in that case disappear" is because the Riddler stole it from Lex Luthor, who got it in Azzarello's other comic about a famous DC comics villain.
Johnny Frost survives
The story seems to be a retrospective account. While it was a realistic take on the mythos,it wasn't that realistic.
- Not necessarily. It could just as easily be a How We Got Here, possibly brought on by the bullet to his face and the realization of his imminent death.
The Joker escaped by blackmailing Arkham's administrator
- When the Joker leaves Arkham, he doesn't escape. He walks out the front gate, without interference. For the rest of the story, he's taking medication which he's supposedly "lived on... for years". How's he getting the drugs? While he could be stealing them, the quiet exit and the constant use (and abuse) of his meds may be linked. Blackmailing Arkham's administrators or his own doctor could easily result in the Joker being able to not only walk out the front gate (with a clean bill of mental health too!), but also getting the drugs delivered to him or easily redeemed thanks to the blackmail victim.
- It could also be Harley who's helped with those two factions. After all, we're not given enough development time on her. It's entirely possible that this takes place before she became a known psycho and thus, it was Harley who deemed him sane enough to leave, and it's Harley who keeps getting the drugs for him to use and abuse.