Your first statement concerning Capcom’s failure to claim a use and its disclaimer seems a bit irrelevant to a copyright claim analysis. While stating a disclaimer would help to protect Capcom from Unfair Competition and trademark disputes, I’m not sure if it’s something a court would rely on for a copyright matter.

Let’s look at the elements of infringement: Access and Substantial similarity.

We know there’s access– Capcom gave that one away with the disclaimer.
Is there a substantial similarity? Ordinary observer test: “whether the accused work is so similar to the plaintiff’s work that an ordinary reasonable person would conclude that the defendant unlawfully appropriated the plaintiff’s protectible expression by taking material of substance and value.” Atari, Inc. v. North American Philips Consumer Elecs. Corp. 672 F.2d 607, 614 (7th Cir. 1982).

First: Is there a protectible expression at issue? We know that ideas aren’t protectible, but a setting, plot, storyline, and theme are all typically considered protectible. So the protectible elements here are arguably: the characters, the mall setting, the types of stores used, the plot, the storyline, the dialogue/script, etc.
Next: Are the two works so similar that an ordinary reasonable person (objective standard) would conclude that defended unlawfully appropriated plaintiff’s protectible expression? A lot of courts rely on the total look and feel approach, so those would likely take your tone argument into account. The ninth circuit uses an extrinsic test: which breaks down both works to their constituent elements, determines which elements of both are protectible and which elements of both are not protectible, and then compare the similarity of the protectible elements. Swirsky v. Carey, 376 F.3d 841, 845 (9th Cir. 2004). So under a 9th circuit analysis, at least, Capcom may need to assert an affirmative defense.
Finally, Was the material used (i.e., the mall setting) of substantial value to the protected work? The use must be substantial in relation to the plainiff’s work as a whole. According to the Supreme Court, a substantial taking doesn’t require a large percentage of the work to be used, but that the defendant took the “heart” of the protected work. Harper & Row Publishers, Inc. v. Nation Enter. 471 U.S. 539, 565-66 (1985). MKR would probably argue that the mall setting was the “heart” of the film, the thing that distinguished Dawn of the Dead from the Zombie genre. Capcom may try to argue scenes a faire, but unless other films/zombie genre games/literature have used shopping malls between Dawn of the Dead and Dead rising, it’d be a bad leg to stand on.

So there is a potential claim here, and it will probably settle, because Capcom doesn’t want to be the one to set bad precedent.