Warner Bros has said that a union of DC characters in a Justice League film is possible, pending the success of Man of Steel at the box office.
Man of Steel has been produced by Dark Knight Rises director Christopher Nolan, leading to speculation that the franchises might be linked to his Batman film trilogy.
Goyer has now clarified that Bale's version of Batman does not in fact exist in the same continuity as Man of Steel.
"It would be disingenuous to say Warner Bros doesn't hope that this would be the starting point for a shared universe," Hey U Guys quotes Goyer as saying.
"And Zack has said that Bruce Wayne exists in this universe. It would be a different Bruce Wayne from Chris' [Nolan] Dark Knight trilogy, and it would be disingenuous to say that Zack and I haven't had various conversations on set, around 'what if' and 'moving forward'."
Goyer also clarified reports earlier in the week that he had already signed on to pen a Justice League script, by insisting that he "definitely" has not formally agreed to any deals for the film.
The writer added that if Justice League moves forward, it will be with "a blank slate" rather than adapting an existing screenplay.
"They're hoping that the film does well, but god forbid it doesn't, things will change. I don't know how many different iterations of Justice League they've tried to mount over the last decade or so," Goyer commented.
"But for one reason or another they haven't happened. I think Warner Bros has seen - and Chris deserves the biggest credit for this - that we were able to revitalise Batman and put it into the first billion dollar superhero film. And they're hoping that Superman will be revistalised as well.
"And if we can do Batman and Superman, then maybe we can move on to Wonder Woman, and The Flash, and characters like that."
It was reported earlier in the week that Warner Bros is already developing a sequel to Man of Steel, as well as projects based around Wonder Woman and Aquaman.
Man of Steel is now playing in US and UK cinemas. Watch Digital Spy's Henry Cavill interview below: