Hmm, that's an interesting point. Personally, I think that if you're explicitly reaching for elementsEqual, you'd probably know the difference, but I do concede that this is only an assumption, and it would be a hard thing to spot a mistake if this did happen even if you did know what you're doing, since it doesn't show its semantics as clearly as a function call.
My thought behind this was that if you're going to write something like what I suggested above, you already know that it won't work on Set, because you understand what the code is actually doing–you wrote it yourself. Personally, I think that's better than any documentation.