That was odd writing from Johns, but I think he was dead. I think Bruce's regret is that he wasn't the one who tried to bring him back. That he just buried him and let him be dead. Because otherwise Bruce buried him alive and that makes no sense.So what even is Jason Todd's Red Hood origin these days? Sounds like in Three Jokers he just wasnt actually 100% dead when they buried him lol. No Talia or Lazarus Pit. Just some dude forget to check his pulse when they buried him?
His origin since Rebirth is basically same as it ever was.They go on a mission, Jason gets killed by Joker, gets dug up by the League of Assassins, then his New 52 component is that Talia takes him to this secret sect super monks to get trained to fight the supernatural.
Jason still becomes an actual villain though at some point first.