So in the config files, within structures (also btw why is this config in structures?) you are meant to be able to choose whether or not you want the normal minecraft villagers to spawn or the pixelmon npcs to spawn, but if you replace "true" with "false" it does literally nothing

That config option is no longer in use, please use allow-vanilla-mobs: false in config.yml. Forwarding the issue to remove the old config option.