I'll never get over the stupidity of how seriously Topps and the brand owners take these things.
Regarding brand owners, I would tend to agree with you, and lets be honest, being parodied on a Wacky Package doesn't seem like the kind of thing that could possibly ever damage a brand.
At the same time, I think being an individual (or a corporation) who works hard to create a brand, one of the things that is part of that is that you get to protect that brand however you see fit, as long as its' legal. And if you want to take your brand too seriously, even if everyone else thinks it's stupid, that's the beauty of owning it.
I think most brand owners simply protect their brands as a rule, and don't see it as a priority to have someone picking and choosing what to let slide and what not to.
I suppose, with the advent of M&M stores and the like, a few of these food companies actually have active intellectual property departments - maybe the cereal companies, too, with the mascots and such - and so probably deal with this kind of thing more often. But how often do the folks at Tombstone Pizza have to worry about how their brand is being used?