Organic society is fully a thought experiment and has very little basis in reality. You are very free to apply the framework of organic society to deep history or existing Indigenous peoples, but that doesn't change its origins as a thought experiment.
In fact, I knew a Lumad man who wanted to apply Bookchin's organic society to his experience and oral history as part of the Kalumaran.
The Neolithic Y-chromosome bottleneck, I guess, doesn't affect Bookchin's ideas much because it's a thought experiment on the emergence of hierarchy, not a serious archaeological work on the Paleo/Meso/Neolithic.