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And Generalplan Touhou (東部総合計画) was a Tengu lie. In reality the Shrine Maiden of the Hakurei Shrine had plans to rather assimilate the Youkai into the Human Race. Of course, some of them, who didn't have the human appearance, were subjects of exile to Makai, but let's be honest it's for the better future. One can not form a functional nation if subjects of it are too different to each other. Total extermination program wasn't a thing, Reimu wanted the Human Race to be a large and prosperous nation and therefore extermination of species alike to humans doesn't make any sense in this scope.
Who Reimu actually wanted to exterminate are Tengu. They sure look human, but they have some facial differencies Youkai don't. Their ears. Their ears are too big to wind any profit they can make with their lies. Tengu like to misinform human folks to cause discords. They want the absolute power.
Smash a Tengu with a rock today.