For instance, GCC will inline functions, unroll loops, and myriad other optimizations that we don't care about. But when we review the ASM that GCC generates (we don't) we are not concerned with the "spaghetti" and the "high coupling" and "low cohesion". We care that it works, and is correct for what it is supposed to do. And that it is a faithful representation of the solution that we are trying to achieve.
Source code in a higher-level language is not really different anymore. Agents write the code, maybe we guide them on patterns and correct them when they are obviously wrong, but the code is merely the work-item artifact that comes out of extensive specification, discussion, proposal review, and more review of the reviews.
A well-guided, iterative process and problem/solution description should be able to generate an equivalent implementation whether a human is writing the code or an agent.