There's no way Brad Frost hadn't seen this. But no shame in the game—great artists steal yadda yadda
How do you know that? It's possible that this obscure reference got lost on the web years ago and he independently came up with the same idea years ago. I don't think that's a fair assessment on your part.
There are several instances of developers and inventors and designers coming up with the same idea separately but around the same time. The recent Spectre and Meltdown exploits was discovered independently by three different researchers.
Brad Frost popularizing and codifying an ethos for Atomic Design is still a benefit for us all. To say he invented it is to ignore great designers in the last who have created such extensive systems for all types of applications. At the same time, ideas DO iterate over time and it would make total sense that Atomic Design presented in 1999 is not exactly the same as Atomic Design talked about today.
I don't. But it's unlikely there wasn't some kind of influence here. The same general concept or idea? Sure—that happens all the time. But the same phraseology, structure and naming conventions? Hmm...
Brad Frost's version is much better IMO.
It's not so outlandish a method or metaphor that it couldn't have arisen in two places independently.