^Don't fall for that shit again. Let's keep this about single-shared-universe vs multiverse-approach and the intelligence of the general audience, shall we?!
Here's the thing: Some people enjoy these movies without giving it much thought. A lot of people have grown to think that Marvel and Superhero is synonymous, hell, even some boulevard show editors like those at Good Morning Britain not that long ago proclaimed Batman a Marvel character (during a segment on his 80th anniversary, too), and this case is hardly unique.
So, even with the last few DC films establishing a connected shared universe, some people even in positions where they maybe should check Wikipedia on such a basic fact, simply assume every superhero to be Marvel. But those people, while obviously enjoying the movies, also obviously don't think that much about them. This is just entertainment to them, thinking about it while the movie is on, then talking with friends about all the cool moments, and that's it.
But those are also just part of the audience. There are obviously enough people who can distinguish between the two companies. And let's not forget, for a very long time, WB/DC didn't want two live-action versions of any one character at the same time, for fear they could confuse the audience. But having The Flash on TV as well as the movies, Superman, too, Batman and related characters in the movies, and younger versions on TV, it has become clear that audiences might get confused for a moment, but those people who care about it either already know of the different versions, or can easily learn about it. It's not like the marketing of "Justice League" tried to make it appear as if Grant Gustin was in the movie.
And, finally, it's also a case of, just try it out. "Joker" has quite a low budget, even if it doesn't make, say, "Shazam!" numbers, it'll do quite well, while also testing the waters for this kind of approach.