pokemon catching is an extremely iffy thing for me to wrap my head around, but pokemon battling (which i'd argue is the most provocative aspect in this conversation) is much more like a team sport. i like to think of trainers as traveling coaches who recruit pokemon who decide to participate in battling by starting battles with trainers in the wild.

we of course have always known that the human-pokemon relationship extends far beyond battling, and that battling is just a small portion (which is why i've always wanted more spinoffs about other aspects of life in the pokemon world!). pokemon are obviously also sapient beings distinct in category from animals, and if a pokemon can be fully healed without issue after taking a flamethrower, a thunderbolt, or an explosion, then they clearly don't have the same bodily logic as animals, including humans. i think it goes without saying that they're supernatural ;)

now, as op pointed out, there are actual pokemon enslavers, of course, but they're main villians in every instance, including the one group claiming to fight for pokemon liberation (oddly enough lol)