The premise, the logic stands on its own. We coevolve with other organisms and bacteria, not in a vacuum. So wether there is hard evidence for this or that, regardless it’s an interesting field of study right now and many are looking into it. Sometimes before you have evidence, you need a hypothesis.

I didn't say anything about the book, I haven't read it. You questioned whether the hygiene hypothesis was a real hypothesis.

According to my very casual glance at the evidence, it appears to be a hypothesis being actively debated by scientists. I'm not sure what else you might want for a hypothesis to be 'scientifically legitimate'.