John Stephens spoke with us a few days prior to Gotham's Season 5 renewal, which was also cemented as its final season on Fox. As such, there may admittedly have been some changes made in the meantime to how Bruce's story goes in Season 5, but then again, Stephens stated the creative team went "full-bore" in crafting Season 4's denouement with the expectations that Season 5 would get ordered. And he definitely had concrete ideas in mind for where things would be heading. So I'd guess that Bruce's identity swaps will still be around, and will hopefully import the actual Matches Malone storyline from the comics. (Just with a different name used, since Gotham already made its own Malone references.)