That linked opinion overstates the case. In the real-world, two different programs performing any non-trivial but functionally identical task will look substantially dissimilar in their source code, and that dissimilarity will carry over to the compiled binary, meaning what was expressive (if anything) is largely preserved. To the extent two different programs do end up with identical code, then that aspect was likely primarily functional and non-copyrightable, or at least the expressive character didn't carry over to the binary. Ordering and naming of APIs in source code can be expressive, and that indeed is often lost (literally or at least the expressive character) during the compilation process, but there are other expressive aspects to software programing that will be preserved and protected in the binary form.

IMO, your intuition regarding AI is right--it's not a magic copyright laundering machine, and AFAIU courts have very quickly agreed that infringement is occurring. But in copyright law establishing infringement (or the possibility of infringement) is the easy, straight-forward part. Copyright infringement liability is a much more complex question. Transformative uses in particular are a Fair Use, and Fair Use is technically treated as an affirmative defense to infringement.[1] If something is Fair Use, infringement is effectively presumed. But Fair Uses are typically very fact-intensive questions, and unlike the case with search engines I'm not sure we'll get to the point where there's a well-defined fence protecting "AI".

[1] There's a scholarly pedantic debate about whether Fair Use is properly a "defense", rather than "exception" to infringement, but it walks and talks like a defense in the sense that the defendant has the burden of proving Fair Use after the plaintiff has established infringement. There's a similarly pedantic (though slightly more substantive) debate in criminal law regarding affirmative defenses. But the very term "affirmative defense" was coined to recognize and avoid these pedantic debates.