The point of much of Thomas' dissent, as I understood it, was precisely that the court is muddying the rules by taking concerns that properly belong in copyrigh

The point of much of Thomas' dissent, as I understood it, was precisely that the court is muddying the rules by taking concerns that properly belong in copyrightability into fair use. They've carved out a subset of copyrights---copyrights on "declaring code"---and made them difficult or impossible to practically enforce. But they did so under one vague fair use factor, not the rules about copyrightability. Because, as Thomas sees it, there's no dignified argument for exclusion or second-class status under the copyrightability rules, most of which come from statute, rather than the courts.