Why do you suppose Pokémon such as Litwick and his brethren, Cofragius, and other people killing/zombifying/enslaving Pokémon and the areas they’ve infested are open to the public? Why hasn’t the (admittedly incompetent) public not restricted the plucky ten-year-old adventurers from entering those areas and risk having their souls and lives put into danger?

I’m going to go with “because then we wouldn’t be able to catch them.”  This sounds like a cop-out, but it has the advantage of probably being the real reason for it, and maybe it can work in-universe as well.  There will inevitably be Pokémon trainers who want to catch these things, and historically would have had the right to take any risks they wanted in order to do so.  Almost all Pokémon can be dangerous if you’re not smart in your interactions with them – Ash almost got killed by a bunch of f$#@ing Spearow on his first day, remember – so once you accept the notion of allowing young people to do this sort of thing in the first place, it becomes difficult to start drawing lines.  Also, training is the first and most important way that people in this world have of interacting with Pokémon, so deciding that trainers aren’t allowed to do so of their own free will probably seems like a really extreme reaction to them – like “holy $#!t, you’re saying that these things are so dangerous we can’t even let the monster-taming nut-jobs near them?  RUN AWAY!”