Looking more closely at the two at the same time issue, Never Say Never Again and Deep Impact were actually profitable, just not as much as their counterparts. You could argue that they were siphoning potential ticket sales from each other, and that may be true, but in Armageddon/Deep Impact's case some of those audience members might never have watched the other one, regardless. Those movies didn't take the same approach to the premise.
If the Joker origin movie is a gritty Scorsese-style drama, and if the Harley Quinn and Joker movie were more about romance and comedy, then they could potentially appeal to different people to a large extent. And since neither really has to be made on a blockbuster budget, then I could see how both could make money, especially if they come out in different years.