Playing the Mega Man Zero quadrilogy was an illuminating experience for how I view Pokemon stories because it made me realize that Actually It's All About Vibes And Aura
PLA isn't really contradicting anything when the Pokedex has been describing their behaviour of some species since the start, like Clefairy and Chansey being very timid, or Mankey/Primeape being very aggressive. Heck, Gold and Silver (and I think some mons in BW) had Pokemon that run away from you, like Teddiursa, Tangela, Delibird, etc.; so the Canalave Library thesis is that, a theory proposed to explain the behaviour of Pokemon, but is not absolute.
PLA using the "humans versus Pokemon" theme so little is a problem, though. It seems at the start and how the game was promoted in trailers that everyone in the village are wary about Pokemon, but you're quickly given sidequests to catch Pokemon for the villagers. They even offer you to take care of your caught mons in a ranch, they didn't commit to this premise whatsoever. Only when not-Rowan kicks you off the village due to paranoia kicking in, but it wasn't well executed.
Since you mentioned the Zero series, one example I wanted to bring up last time about how wasted LA's "humans vs Pokemon" angle feels is from that series. I didn't mention it before bc I didn't know if you were familiar with them. So here I present, the Caravaners from Zero 4.
View attachment Caravan.webp
The Caravaners are people from Neo Arcadia, once a paradise for humans, escaping from Weil's tyrannical regime and settling in the life resurging Area Zero. After all the wars in which the humans got caught in the crossfire, they've grown to dislike all reploids, including Zero and the Resistance. Some of them (the younger ones) act timid were Zero meets them, others (the grown ups) are more hostile. Their leader Neige is less prejudiced because she was saved once by a reploid, Craft, and became
lovers friends but she's still cautious around Zero.
At the halfway point of the game, the Caravan is invaded by Weil's forces and Zero goes to the rescue. Craft, now serving Weil, kidnaps Neige after she reveals they used to know each other; and the caravaners are willing to abandon her because of this, despite all the help Neige provided them and that their camp was just saved by the resistance. This was Zero's last straw, he calls them out for their cowardice and goes to rescue Neige himself. The caravaners realize their mistakes and act more open towards Zero from then on, they even start believing again in a world where humans and reploids can live together like they used to in the Classic and X series, which is doubly heartwarming considering that's what happens in the ZX games.
The caravaners are like the Jubilife villagers, both groups are afraid of what the other faction (Reploids and Pokemon) did to them in the past, and feel threatened around them, except it's more clear in Zero 4 that you are not welcome at the start. In Legends Arceus it's kinda hard to believe ppl are feeling threatened about Pokemon no matter how much they say it at the start, when Jubilife Village still behaves like the usual Pokemon world, with professors passionate for investigating Pokemon, clan leaders and wardens respected figures like gym leaders will be in the future, and just how quickly you're given quests to introduce Pokemon to the village.