It’s also worth mentioning that the Scarlet dex entry of foongus says “There is a theory that the developer of the modern-day Poké Ball really liked Foongus, but this has not been confirmed.” It’s not a direct confirmation, but it makes it seem more likely that the pokemon came first imo
All they'd actually have needed to do is retcon Apricorns to have a bi-color look* during L:A, and suddenly it all makes sense. Various things eat Apricorns, Foongus/Voltorb look like Apricorns to catch prey**, humans turn Apricorns into pokeballs, later balls keep the same design out of tradition, Foongus/Voltorb evolve over time to match the new design. Solve the problem and flesh out the natural world at the same time.
*Or state that modern White/Blue/Black/etc Apricorns are the result of selective breeding by humans and the OG Apricorns were White+Red
**Why Voltorb, whose primary reaction to meeting anything is to blow itself up, looks like something people WANT to interact with, has never been satisfactorily explained, but that's not new.
Wait, scratch all of that. Voltorb reacts really badly to being interacted with and Foongus is slow and toxic. They don't have Pokeball colors for disguise, they have them as a warning. "I'm red+white, colors that camouflage with nothing when together. Come near me and die." Which would mean humans modeled our balls after dangerous-to-approach mons(presumably so that if you drop your ball in the wild nothing plays with it), and then those mons evolved to look more like our balls after wild mons learned that the human's Red+White balls are dangerous.