I believe Justice Thomas agrees with your assessment, and he raises concern that the SCOTUS has essentially made APIs practically uncopyrightable (in that they will 100% of the time find that it's fair-use to use them).
That would seem a reasonable outcome, for much the same reason that copyright not protecting the appearance of fonts under US law is reasonable. Yes, it is overriding copyright protection for a creative work that would otherwise apply. However, it does so because a greater good is served, in this case by ensuring that interoperability cannot be encumbered, something which (as the majority opinion alludes) goes against the very purpose of copyright under US law.
The main legal basis for the majority opinion seems to be fair use, so isn't the system operating as intended? The legislators set out a principle of fair use in statute. The court applied that principle in the context of this specific case.
That would seem a reasonable outcome, for much the same reason that copyright not protecting the appearance of fonts under US law is reasonable. Yes, it is overriding copyright protection for a creative work that would otherwise apply. However, it does so because a greater good is served, in this case by ensuring that interoperability cannot be encumbered, something which (as the majority opinion alludes) goes against the very purpose of copyright under US law.