In the original scene from Ultimate Fantastic Four #32, Doctor Doom is shown appearing through a portal. In the scene from Marvel Zombies vs Army of Darkness #5, no counterpart to Ultimate Doom arrived (Ash arrived in a different area). This could either mean a counterpart to Ultimate Doom arrived later, or events for the Fantastic Four of the Werewolf reality (and whatever Earth they tried to invade) went differently.
Curiously in this universe, Captain America (or possibly this world's version of Colonel America) and Black Widow are seen alive while Iron Man isn't. It could be assumed that since these are werewolves instead of zombies, events went much differently in the Werewolf Reality than they did in the Marvel Zombies Reality. A zombie Iron Man, being undead, would survive being blasted in half by the Silver Surfer while a werewolf Iron Man likely wouldn't.
Captain/Colonel America, Luke Cage, Spider-Man, and Wolverine show no signs of similar injuries that their Earth-2149 counterparts received. Since werewolves have regenerative healing ability and enhanced agility while zombies don't, it's assumed that the injuries the Marvel Werewolves received was minimal or easy to recover from due to their healing powers.
Captain America being a werewolf could also be an intentional reference to CapWolf.