Just a few Theories.

[Diz-Infinite]

Okay, I have a few theories of the zombies. I would like to first point out that SOMEONE or SOMETHING has to be controlling them. As the Mobsters still can get drops, hear the voice from the drops, and someone has to summon Brutus. So the argument that no one does in unlikely.

THEORY ONE: Maybe, just maybe, the teleporters from Der Rise had sent someone back to the 1920-30's. Maybe an unintroduced character. Maybe Maxis himself. Maybe another unmentioned colleague. Or maybe even Samantha, when she was in control, had the ability to time travel. Her having the ability would explain why the perk machines are there, because she could have taken them back with her. (Except the Electric Cherry per which is the only perk that doesn't phase in and out, which may have been there originally.) However this doesn't explain why their eyes are changed.

THEORY TWO: Perhaps the zombie experiments went on before Nacht Der Untoten, and Dr. Maxis may have been friends with the Warden. Maxis may have been paying big money (compliments of Group 935) to have some experiments done on the inmates of Alcatraz. Of course Maxis himself couldn't be there in person, so the Unnamed Warden could have taken the zombie control for himself. (Brutus, based on attire, isn't the warden. He's likely a head guard, or riot guard.) This would in turn make the zombies eyes red, being its a new master.

THEORY THREE: in Die Rise, you hear of a "rift". As it seems, this could be a rift in time, a rift into an alternate universe, or a rift between Richtophen and Satan. The rift in time supports my first theory. The second rift though, to an alternate universe could lead to a whole other world and storyline of Zombies. Richtophen may want to try to control zombies among a span of universes. The mobsters being in the alternate one, resulting in red eyes. A rift between Richtophen and Satan, could mean Rich wants to control Satan's power, to become stronger, and omnicient. This would explain a lot of the more evil and dark features in Alcatraz. (E.g. The hanging bodies, the hellhound heads written in blood, the "666" that appears several times) He may have lost the battle and Satan controls the zombies, or won, and SatoRichtophen controls them. (Of course he would still need to travel back in time for this to make sense.)

These are just a few thoughts. We can't know for sure until new clues are discovered, or the next map. Hell, for all we know, it could be completely non-canon, and just a test for the new features.