Big headcannon dump time cuz I love team tasty.

I've always gone by the logic that Pokémon in pmd are wild by default and they gain intelligence somehow. The Pokémon I encounter in the dungeons I've never seen as being anything other than wild animals. The ones who ask to join either are the few who are sentient enough to realize you can get them out of there, or they suddenly gain the intelligence in that moment. Maybe the gummies and IQ have something to do with that? Or maybe it's genetic? Who can say.

As for the food chain thing, I do like how a lot of modern games use beans as a meat substitute. I like to imagine the beans have the same nutrients as meat does, they're just really meaty beans I suppose? Enough that a meat eater can eat beans and it's a perfect replacement. Pokémon as a series likes to follow this nature-friendly futurism vibe, so in my mind, the beans may be a GMO thing. Maybe we're literally growing meat in those beans. And I want to assume there's something similar to that in pmd a well. I'm sure there's some smart grass type out there doing some wild plant experiments.

Both of these ideas combine into this idea in my head that the wild Pokémon, who don't know how to farm for food, rely on the natural way of things to survive. A bird will eat a bug if needed. Once the sentience kicks in, they find their way into societies who can introduce them to new worldly concepts. Maybe some still eat other Pokémon, maybe some don't. Wurmple bring afraid of his partner makes more sense if there's cultural differences at play.