Unlike animals, many pokémon are indeed capable of consuming a diet very similar to that of humans, which means many things that would be toxic to their “animal counterparts” are actually not toxic to them. Chocolate is probably the most noteworthy example; while it may be extremely dangerous for canine animals to consume, it’s perfectly harmless for the riolu line, the zorua line, and many others.
Of course, just because a pokémon species can eat it doesn’t mean it should or that every member of the species can. Zorua, for example, are primarily carnivores, so while waffles are fine as an occasional treat, they need a healthy diet of meat and leaner grains and vegetables to survive. If one consumes nothing but waffles for several of its meals a week, it won’t necessarily kill them, but it will be the equivalent of a human being surviving on nothing but candy and instant ramen—which, no, one cannot do. I may or may not know this from experience.
Likewise, while many species have no problems mixing human food into their diets, other species absolutely cannot. These tend to be the more delicate species or species that rely on diets of items that aren’t edible to a human at all. Sableye, many rock-types, most steel-types, and the sunkern line, for example.
Additionally, it’s entirely possible for members of certain species to acquire the inability to consume certain foods. Cat-like pokémon, for example, may become lactose intolerant after weaning (contrary to popular belief). Not all cat-like pokémon become incapable of consuming dairy, however, so knowing whether or not yours can requires keen observation on your part.
That is perhaps the main thing to keep in mind concerning pokémon nutrition, actually: always observe your team members and take note of their habits, their physiology, and their pokédex entries. While it’s true that larvitar may not consume entire mountains, it’s still sound advice to feed yours a diet rich in minerals. The more you study your own pokémon and information about their species, the better armed you’ll be when it comes to taking care of them.
As for your zorua, in the end, it’s all right to feed her waffles now and then but don’t make it a habit unless you’d like a pudgy zorua with a whole list of regrets.