It seems to me, when you're counting things, you wouldn't care what are the things you're counting specifically; while in your example it does matter for determining the subset relation. Whatever way of counting where it matters would be kind of weird.
> it seems like an unwarranted leap to go from this formal comparison of cardinality of infinite sets, to the intuitive English-sentence idea that "almost all" real numbers are irrational
But the article uses "almost all" in the formal sense? Which, by the way, also has pretty intuitive meaning, in my opinion.