Oh, yes - that thought had occurred to me sometime last night. With the way things are going comic!DCUwise, this is definitely a different continuity. Your theory could still be a valid one, if you consider the possibility that the 'Joker' Batman & Nightwing faced could've been Tim who was taken over via the microchip DNA for a short period of time. The Joker even admitted himself that he had to limit the time he spent in Tim's body, the latter contributing anything the former did to bad dreams.