The news that Warner Bros. was working on two separate Joker movies, with two different actors playing the character in each, was met with confusion. The company's DC Extended Universe is still relatively new, and only recently started picking up momentum thanks to "Wonder Woman." Introducing a whole new series of unrelated DC titles might confuse casual audiences, stopping any chance the DCEU has of Marvel-like mainstream success.
There is one way they could make it work. All they have to do is take inspiration from the comics these movies are based on, specifically, the "Justice League" comics, where Batman recently learned there were three jokers. In last year's "DC Universe Rebirth #1," he can be seen studying three photos of The Joker on the Bat Computer. They are very clearly three different people.
Adopting a similar story would allow Warner Bros. to make both Joker movies and avoid some of the confusion. Moviegoers wouldn't have to ask whether the movie they're seeing is connected to "Justice League" or not before buying a ticket. The upcoming untitled Joker and Harley Quinn movie with Jared Leto and Margot Robbie is about one Joker, while the origin story starring a different actor is about another.
They both take place in the DC Universe, but they're two different characters.
Warner Bros. wants to ensure their superhero universe is different from Marvel's. The ability to have standalone movies that don't feed into a massive crossover is one way to accomplish that, as long as they can keep they're stories straight. This might be the one instance where cribbing a comic book story could make things less confusing.