No i don't think Affleck is making another film. I think he keeps saying that because otherwise it would be a PR disaster. Ben Affleck is an acclaimed director and actor. After he won the Academy Award DC actually made a coup by getting him for Batman. I am noticing things which says that he is not interested but going away. First, he was supposed to direct as well as act in Batman. Then he said he wants to do the role justice so he is stepping away from the director's chair. A while back there was something like he wants to gracefully segue out of the role. For someone of his talent who has risen out of a slump in career to be part of DCEU makes no sense even if he is a big fan of these characters. Imagine if he had said i am leaving playing Batman in March or even a month or two ago. It would cast a really bad light on WB and DCEU.
People aren't so confused with these continuities. Even a little thinking makes big holes in X-Men franchise. People seem to be doing fine with it. And yes Deadpool and X-Men are in different continuities. Deadpool lives in a universe which has the X-Men. But they are not shown and are actually different. There's a different Colossus there who is different from other X-Men films.
Inhumans and Iron Fist are tv series. They are not so problematic. DC has been having failures since Man of Steel. If MoS, BvS, SS would have been successful no matter what JL would have been in the top 10 highest opening weekends among comic book films at least. At present its at #22. Just behind the original Guardians of the Galaxy. They did not come even for Wonder Woman.
http://www.boxofficemojo.com/genres/...er=DESC&p=.htm