Perception was kind enough to upload a case study of their work on Batman v Superman this week. That case study includes a map of the Metropolis-Gotham region as envisioned for the movies DC and WB have been making.
That map clearly does not hew to the maps of the two cities as published in the comics over the last couple of decades. Granted, the production team had the right to plant the two super-cities ten miles and a harbour apart from each other. Speaking for myself alone, I'd hoped that Byrne's Six Boroughs as originally drawn up for Metropolis in 1986, as well as the islands of Eliot Brown's 2000 map of Gotham could've made the cut.
Oh well...this is its own thing to begin with.