No doubt, and separate organs with (sometimes rough, sometimes very clear) separate functions are also a thing, so evolution seems to favor compartmentalization

No doubt, and separate organs with (sometimes rough, sometimes very clear) separate functions are also a thing, so evolution seems to favor compartmentalization for more complex systems. But that does not mean that there are not complex overarching interactions that make full understanding really hard. The sort of interactions you would stay away from when designing a computer, not because it would not work, but because it would make design, debugging, and iteration upon your system prohibitively hard.