Notice how there's only one team composition here. Yes, that's to be expected that NPC Trainers all have their teams made well in advance. So, what's the problem here? The problem, as I see it, is that several of them will use version-exclusive Pokémon on their teams even if you can't find this Pokémon in the wild in the version you're playing. From a gameplay perspective, I would imagine this was most often done for the sake of allowing players to have these Pokémon registered as "Seen" in the PokéDex regardless of if they can actually be obtained. Somewhat similarly, we have Pokémon such as Cynthia's Spiritomb in the Sinnoh games, who I'd be willing to bet was the only reason most players could eventually get that PokéDex sighting logged if they didn't have access to people to play in the Underground with. From a world-building perspective, however, this is where things start to fall apart. We know because of several datamines as well as the GameCube Pokémon games that NPC Trainers also have their own OT designations, meaning that we can naturally assume the Pokémon used by NPC Trainers were not specifically traded to them unless otherwise specified.
So with that in mind, using RBY/FRLG Misty as an example again, in the versions where Staryu and Starmie can't be obtained... where the heck did she get these Pokémon from? They couldn't have been found in the wild, as we've established, but they also couldn't have been traded to her since they're still internally recognized in the games as Misty's own Pokémon. I'm not asking for these games to be as realistic as possible, but from an in-universe perspective, there should be absolutely no reason Trainers do this so often. What's even more stupid to me is that the vast majority of the examples I could think of off of memory have other Pokémon that they could be replaced with for those versions. The most recent example I can think of where a game did this right was with Milo's rematch team in Sword & Shield, where two of his team members are actually different in each version which includes his G-Max Flapple/Appletun respectively.
(Disclaimer: If you try and cheat and catch an NPC's Pokémon during a battle, more often than not the game will try and treat it like a wild Pokémon encounter as a sort of failsafe. I know this because I've tried it before with Action Replay codes as a kid.)
