So, I think you are right that computer software problematisizes much of copyright law, and this is how we get to this confusing situation.
But to be clear, instruction booklets are copyrightable, but the _instructions_ are not. (Or haven't been prior to this case? I think some worry that if the logic of this case if carried through, many things that were previously not protected by copyright will become so).
Let's say you figure out, say, a great new way to assemble some tool, and write down instructions for it (1. Get a ball of twine. 2. Get some chewing gum. 3. Affix the chewing gum to twine.)
Your instruction booklet itself is copyrightble -- nobody can photocopy it without your permission. But the steps you figured out are not copyrightable, someone else can write down those steps in their own words, hey, look what we can do with chewing gum and twine, and that is not protected by copyright. You can't stop someone from sharing those steps with others in their own words, and you can't stop someone from carrying out those steps. (Under copyright, that is. The steps may be patentable; that's a different law. But they are not copyrightable. Or... didn't used to be?).
That's the way copyright has been. It seems to many that the API itself, and the ability to make new software with the same API, is more like "following the steps yourself in your own words", than it is like the "instruction booklet." If someone writes docs for their API with lots of good narrative instructions and examples -- nobody else can just copy that documentation ("instruction booklet") wholesale, that's protected by their copyright, nobody disputes that. But the classes, methods, and signatures themselves, prior to this case, most everyone thought were more like "steps themselves" and not subject to copyright.
An "an understanding between people" has in fact never been copyrightable in itself, you can't stop someone else from sharing the same understanding, under copryight. You could stop someone else from copying particular text describing that understanding, but only the particular text.