The two-part animated adaptation will end with Superman donning one of his Rebirth costumes.
The War-verse has to catch up to the comics somehow.- It may even end with him donning the classic comics costume, red trunks and all, since he's wearing that again in Action Comics #1000 and the fans want it back anyway.
Intergang is a Chekhov's Gun.
They weren't just there for a Batman Cold Open. In Reign of the Supermen they will turn out to have an important effect on the plot. (This WMG stems from the fact that in the first film, they're just kind of... forgotten, after the first few scenes, despite the investigation into them not being really resolved).