Earth-9602, Earth-496 and Earth 1996 all refer to the exact same reality but in different multiverses. The thinking is that Earth-96 is supposed to be the reality of the Superman film series, including III-IV, and Earth-789 includes III-IV. One could easily argue that no universe merging happened and that Earth-89 includes Superman I-IV, and Earth-96 doesn't include I-IV despite the intention that it was supposed to I guess.
I don't agree with the idea that there's lots of Crisis changes though. Pre-Crisis Earth-89 and Earth-96 can be alt. versions because they get destroyed, and post-crisis is the real Donnerverse. There doesn't have to be any other changes here.
But... he goes from having Christopher Reeve's face to Brandon Routh's and then to Reeve's again in The Flash (the movie). I know it is not so confusing:
Pre-Crisis:
-Earth-89 - Batman I-II + Catwoman
-Earth-96 - Superman I-IV + Returns + Supergirl + Joker in Daily Planet (Was it ever called officially Earth-78 or did fans deduce it from Earth-66, Earth-89 and Earth-97 designations?)
Post-Crisis:
-Earth-96/789 - Batman I-II + Catwoman + Superman I-IV + Supergirl + Returns + Joker doesn't massacre the Daily Planet
Flashpoint (DCEU, not Arrowverse)
-Earth-1-Flashpoint - Batman I-II (?) + The Flash
-Earth-96(?) - Superman I-IV + Supergirl
Post-Flashpoint
-Earth-96/789 - Back as Post-Crisis?
But the fact that characters changing actors is a plot point in The Flash makes me start wondering if there is more in there, even if it wasn't the intention.
Hum... It is the fact that the Joker of Earth-96 merges with his Earth-89 counterpart, that is dead by time of the Daily Planet massacre, the thing that prevents it from happening?