The general consensus of the online articles I've read is that Reeves probably doesn't mean the Batman film will be in a separate continuity, just that it'll be a self-contained film like Wonder Woman, telling its own independent story within the universe, rather than having a lot of crossover and connective tissue with other DCEU films like BvS did. In other words, it'll be done the way the comics are usually done (or the way the Arrowverse TV shows are done), with the individual series just telling their own stories most of the time and only crossing over occasionally.