When you say that, "Centralization has an optimal scale (most times not so rationally clear), and growing beyond it can fragilize the whole system, generate excessive efficiency and eliminate needed redundancies," that's very close to the point of the Iron Law of Oligarchy.

The point is that the centralization of power makes for a more efficient organization of the parts and thus of the system. Your point is that there's a trade-off between efficiency and flexibility. Indeed, in social systems, centralized power is often corrupting, which is a mechanism of inflexibility. I'm not sure, though, what systems theory would add to that kind of analysis unless there were a more general, physical point to be made.

A self-organizing system has to be managed or it will collapse. Management can be efficient or inefficient, and each strategy may have its advantages and drawbacks. But the more decentralized the control mechanisms, the less coherent the system might be. The system would resemble a field rather than a unified system. Think of a democracy as compared to a dictatorship.

And systems like capitalism that are supposed to be decentralized end up forming monopolies that centralize power, as the system self-organizes and becomes more coherent and distinctive, but also, as you say, more fragile and vulnerable to conflict with the environment.