The three Jokers were the clown, the mastermind, and the comedian, and I think they were supposed to represent the different Jokers from the different eras of his comic book history, so the Golden Age would be the mastermind, or the Joker of Earth 2, the Silver Age Joker would be the clown, or the Joker of Earth 3 (my favorite part of the Batman multiverse, by the way), and the Bronze to Modern Age would be the comedian, or the Joker from the main timeline. The Joker of the main timeline is the one who killed Jason in the comics, because the other stories did not take place in other parts of the multiverse, and all three Jokers are probably still alive, because it's heavily implied in the comic that the two other Jokers the comedian was with were fakes (although, in the Forever Evil storyline, Owlman claims to have killed the Earth 3 Joker, so maybe they aren't all still alive).
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Overall, the comic kind of added some extra layers to the Joker's character, but I don't like that they retconned his wife and child being dead at the hands of the mob, especially since in the Return of Hush comic, Joker was even willing to team up with the Riddler to find her killer! I guess we can't have a sappy return-to-the-Silver-Age story featuring the Joker, can we? Well, there are Elseworlds and fanfiction, I guess.
I think the comic would have been better if Joker were actually working with his counterparts from other Earths. It would show that Joker is aware of the multiverse and capable of manipulating the people in it to his ends, as well as give Batman some fresher Joker-centric challenges to face. They could also not make Joker the main villain for most of the series and just have Joker interacting with his counterparts as fun side stories until the reveal that he set the whole thing up. That would shine the spotlight on the clown and the mastermind a bit more.