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To What Extent are Humans Optimized?

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The left recurrent laryngeal nerve and the vas deferens are classic examples of suboptimal anatomical features. One might imagine there are structures in the brain that are suboptimal in a way that is analogous to the left recurrent laryngeal nerve and the vas deferens. Perhaps there are some we have yet to recognize as such because we don't understand how the brain works.

minimizing how many instructions you need to add to the genome in order to make something happen

This is the mechanism for why the body isn't fully optimized: it has to be backwards compatible and build iteratively off of previous DNA. That tech debt is exactly what an artificial engineered brain/body could re-design.

That makes sense, direct editing is going to cause a lot of indirect problems. Similar to immune system or dietary supplements.