Question is, whether those older parts are best viewed as legacy infrastructure, or as ASICs - parts that are in their local optimization minimas for functions they perform, and better than a uniform architecture?
I mean, a lot of the "older" brain is control circuitry that keeps everything running and regulated without our conscious thought. Everything will have that -- at some level. It might just be actual control circuitry and not anything tied to the "brain" (e.g. a PSU in a computer), but the function would need to be performed, and if it's not part of the brain, the feedback we get (e.g. about stress or pleasure) might be lost?
I think that a lot is control circuitry, like the bits that regulate digestion or body temperature. I don't see any reason that for a superintelligence these could not be consciously controlled. The main reason we have so many unconscious processes and heuristics in our brains is to limit the total power consumption, as that was super important back in the days when food was scarce. If power consumption becomes less important, you could do more and better thinking.
It doesn't require a superintelligence. It's possible to gain a certain amount of control over various unconscious processes by means of mental-training.