There was a bunch of stuff referenced, explained,and implied when they met Bill at the Lighthouse early on in Kanto that basically was never referenced again. 7th+captures with a full party getting automatically transferred back to...somewhere, Mewtwo being on Bill's door, the on-going sub-plot of Giant Anime Pokemon (and the implication that Dragonite was an unknown Pokemon), and a bunch of other stuff.
I think it's a good theory saying these rules only apply to those with Pokedexes and participating in some sort of competitive league. We've seen many grunts for evil teams carrying around dozens of Zubats, for example. And keep in mind, Pokedexes seem to be easier to get in the anime. In the games, they're very, very rare, and are a work in progress. In the anime, the Pokemon a trainer sees is likely to already be identified and have info on it.