Yes, but I would venture to say that the vast majority of web applications don't need multi-threading. In all of my years as a web developer I have never had the need to spin off multiple threads to accomplish something. I know that doesn't mean it does not happen, however, I don't think it's a terribly major point that you're making.
Multi-threading is very cool and I wish I had more of a need for it because I think it's just plain fun, however, I can't see it as an absolute necessity for web development.
There's truth to your argument and maybe a feature by feature comparison would show Java as the clear winner, however, the author's point is more about PHP's ability to scale and the fact that many people think it can't. Multi-threading (other than in the web server itself) won't help scalability much.