This movie is deeply, deeply, warped and twisted, and pretty damned magnificent (Hamill, Friedle and Conroy firing on all cylinders, and the new Batman's taunting of Joker is awesome)
THIS is what "The Last Laugh" crossover should have been. If the Joker were worried about his mortality, the last thing he'd do is make dozens of Joker's to dilute his name. But turning Batman's son into his own heir is a magnificently sick idea. The idea of deliberately kidnapping a child to torture him to insanity and into L'il J here is possibly the most grotesquely ghastly thing the Joker has been seen to do.
And weirdly, the CUT version is, as regards what happens to Tim, worse. The Uncut version has the Joker mentioning that he used truth serums and drugs on Tim to get him to confess Batman's ID, whereas the CUT version has him simply be tortured until he cracked.
The Uncut version of the Joker's death IS vastly superior to the cut version, where it is almost embarrassing.
As for Dick's absence from RotJ, well. I have my own theory about that, which I put into a fanfic I've just posted here