I interact with people who seem about as smart as me fairly often- my college professors for example. And, I certainly have been in many situations where my domain knowledge was vastly less than some other person with real expertise. But I have a hard time thinking of a time when I thought someone else was significantly smarter than me. Probably, that's an example of exactly what the article is talking about- maybe I've met those people but failed to recognize them. They certainly must be out there (unless i am the smartest person in the world, in which case we're all in serious trouble).
A few signs: they know what your about to say and give you refutations to your argument before you voice them. Or you find they tend to block your argumentation and you don't quite know how to respond. Could be domain expertise though.
Or if it's a collaborative situation, they might propose an idea you are already kind of thinking about, but they do it faster and clearer.
Similar to your observation - I can think of at least one person who is definetly a lot smarter than than me, and yeah, I’m not sure I could tell you why exactly.
Part of it looks like focus, I think I have a broader skill set than they do. But I don’t know that I could like rank a set of people smarter than me.