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The actual EU statement is still weaker than what the Ars article makes it out to be. One notable example is that there is such a thing as compilation copyright, a cookbook can be copyrighted even though recipes cannot. In much the same way the EU is saying that you cannot copyright small APIs, for much the same reasons why you can't copyright recipes, but a greater integrated work fall into a different category. The Oracle suit fits this shape nicely, being about 37 (relatively few) disparate classes, and got appropriately shut down.

I would suspect that for example you cannot implement the entire interface of Emacs without respecting the GPL, since the public API is actually the entirety of the editor (it exports largely all its internals, and you can figure them all out by introspection from within the editor). It would simply be an obvious rip-off of a lot of work from GNU contributors, and would not really serve the purposes of simply making something Emacs-compatible. Implementing an editor that exports the same user-facing functions (the subset of Emacs functions that are prepared for being bound to the keyboard), and a compatible elisp environment (the documented parts of the interface that is expected to be used by package developers) would be fine, but ripping off the rest of the structure of Emacs would not be. It might be tempting at that point to define "API" to not cover the rest of the functions, but these functions are just as accessible as anything else, and the GPL would allow anyone to make a fork of Emacs that exported even the remaining inaccessible structure as APIs.

This is to some part speculation, but it is more or less how I would expect the line to be drawn. At the very least it is important to remember that there are no special rules for programming in copyright law, it all falls under the usual idea/expression and fair use rules as everything else.